The term bioarchaeology has been attributed to British archaeologist Grahame Clark who, in 1972, defined it as the study of animal and human bones from archaeological sites. Redefined in 1977 by Jane Buikstra, bioarchaeology in the United States now refers to the scientific study of human remains from archaeological sites, a discipline known in other countries as osteoarchaeology, osteology or palaeo-osteology. Compared to bioarchaeology, osteoarchaeology is the scientific study that solely focus on the human skeleton. The human skeleton is used to tell us about health, lifestyle, diet, mortality and physique of the past. Furthermore, palaeo-osteology is simple the study of ancient bones.
In contrast, the term bioarchaeology is used in Europe to describe the study of all biological remains from archaeological sites. Although Clark used it to describe just human remains and animal remains (zoology/archaeozoology), increasingly modern archaeologists also include botanical remains (botany/archaeobotany) 
Bioarchaeology was largely born from the practices of New Archaeology, which developed in the United States in the 1970s as a reaction to a mainly cultural-historical approach to understanding the past. Proponents of New Archaeology advocated using processual methods to test hypotheses about the interaction between culture and biology, or a biocultural approach. Some archaeologists advocate a more holistic approach to bioarchaeology that incorporates critical theory and is more relevant to modern descent populations.
If possible, human remains from archaeological sites are analyzed to determine sex, age, and health. which all fall under the term 'Bioarchaeology'.
Paleodemography is the field that attempts to identify demographic characteristics from the past population. The information gathered is used to make interpretations. Bioarchaeologists use paleodemography sometimes and create life tables, a type of cohort analysis, to understand the demographic characteristics (such as risk of death or sex ratio) of a given age cohort within a population. Age and sex are crucial variables in the construction of a life table, although this information is often not available to bioarchaeologists. Therefore, it is often necessary to estimate the age and sex of individuals based on specific morphological characteristics of the skeleton.
The estimation of age in bioarchaeology and osteology actually refers to an approximation of skeletal or biological age-at-death. The primary assumption in age estimation is that an individual's skeletal age is closely associated with their chronological age. Age estimation can be based on patterns of growth and development or degenerative changes in the skeleton. Many methods tracking these types of changes have been developed using a variety of skeletal series. For instance, in children age is typically estimated by assessing their dental development, ossification and fusion of specific skeletal elements, or long bone length. For children, the different points of time at which different teeth erupt from the gums are best known for telling a child's age down to the exact year. But once the teeth are fully developed, age is hard to determine using teeth. In adults, degenerative changes to the pubic symphysis, the auricular surface of the ilium, the sternal end of the 4th rib, and dental attrition are commonly used to estimate skeletal age.
When using bones to determine age, there might be problems that you might face. Until the age of about 30, the human bones are still growing. Different bones are fusing at different points of growth. Some bones might not follow the correct stages of growth which can mess with your analysis. Also, as you get older there is wear and tear on the humans' bones and the age estimate becomes less precise as the bone gets older. The bones then become categorized as either 'young' (20–35 years), 'middle' (35–50 years), or 'old' (50+ years).
Differences in male and female skeletal anatomy are used by bioarchaeologists to determine the biological sex of human skeletons. Humans are sexually dimorphic, although overlap in body shape and sexual characteristics is possible. Not all skeletons can be assigned a sex, and some may be wrongly identified as male or female. Sexing skeletons is based on the observation that biological males and biological females differ most in the skull and pelvis; bioarchaeologists focus on these parts of the body when determining sex, although other body parts can also be used. The female pelvis is generally broader than the male pelvis, and the angle between the two inferior pubic rami (the sub-pubic angle) is wider and more U-shaped, while the sub-pubic angle of the male is more V-shaped and less than 90 degrees. Phenice details numerous visual differences between the male and female pelvis.
In general, the male skeleton is more robust than the female skeleton because of the greater muscles mass of the male. Males generally have more pronounced brow ridges, nuchal crests, and mastoid processes. It should be remembered that skeletal size and robustness are influenced by nutrition and activity levels. Pelvic and cranial features are considered to be more reliable indicators of biological sex. Sexing skeletons of young people who have not completed puberty is more difficult and problematic than sexing adults, because the body has not had time to develop fully.
Bioarchaeological sexing of skeletons is not error-proof. In reviewing the sexing of Egyptian skulls from Qua and Badari, Mann found that 20.3% could be assigned to a different sex than the sex indicated in the archaeological literature. A re-evaluation of Mann's work showed that he did not understand the tomb numbering system of the old excavation and assigned wrong tomb numbers to the skulls. The sexing of the bone material was actually quite correct. However, recording errors and re-arranging of human remains may play a part in this great incidence of misidentification.
Direct testing of bioarchaeological methods for sexing skeletons by comparing gendered names on coffin plates from the crypt at Christ Church, Spitalfields, London to the associated remains resulted in a 98 percent success rate.
Sex-based differences are not inherently a form of inequality, but become an inequality when members of one sex are given privileges based on their sex. This stems from society investing differences with cultural and social meaning. Gendered work patterns may make their marks on the bones and be identifiable in the archaeological record. Molleson found evidence of gendered work patterns by noting extremely arthritic big toes, a collapse of the last dorsal vertebrae, and muscular arms and legs among female skeletons at Abu Hureyra. She interpreted this sex-based pattern of skeletal difference as indicative of gendered work patterns. These kinds of skeletal changes could have resulted from women spending long periods of time kneeling while grinding grain with the toes curled forward. Investigation of gender from mortuary remains is of growing interest to archaeologists.
Enamel hypoplasia refers to transverse furrows or pits that form in the enamel surface of teeth when the normal process of tooth growth stops, resulting in a deficit of enamel. Enamel hypoplasias generally form due to disease and/or poor nutrition. Linear furrows are commonly referred to as linear enamel hypoplasias (LEHs); LEHs can range in size from microscopic to visible to the naked eye. By examining the spacing of perikymata grooves (horizontal growth lines), the duration of the stressor can be estimated, although Mays argues that the width of the hypoplasia bears only an indirect relationship to the duration of the stressor.
Studies of dental enamel hypoplasia are used to study child health. Unlike bone, teeth are not remodeled, so they can provide a more reliable indicator of past health events as long as the enamel remains intact. Dental hypoplasias provide an indicator of health status during the time in childhood when the enamel of the tooth crown is being formed. Not all of the enamel layers are visible on the surface of the tooth because enamel layers that are formed early in crown development are buried by later layers. Hypoplasias on this part of the tooth do not show on the surface of the tooth. Because of this buried enamel, teeth record stressors form a few months after the start of the event. The proportion of enamel crown formation time represented by this buried in enamel varies from up to 50 percent in molars to 15-20 percent in anterior teeth. Surface hypoplasias record stressors occurring from about one to seven years, or up to 13 years if the third molar is included.
It was long assumed that iron deficiency anemia has marked effects on the flat bones of the cranium of infants and young children. That as the body attempts to compensate for low iron levels by increasing red blood cell production in the young, sieve-like lesions develop in the cranial vaults (termed porotic hyperostosis) and/or the orbits (termed cribra orbitalia). This bone is spongy and soft.
It is however, highly unlikely that iron deficiency anemia is a cause of either porotic hyperostosis or cribra orbitalia. These are more likely the result of vascular activity in these areas and are unlikely to be pathological. The development of cribra orbitalia and porotic hyperostosis could also be attributed to other causes besides an iron deficiency in the diet, such as nutrients lost to intestinal parasites. However, dietary deficiencies are the most probable cause.
Anemia incidence may be a result of inequalities within society, and/or indicative of different work patterns and activities among different groups within society. A study of iron-deficiency among early Mongolian nomads showed that although overall rates of cribra orbitalia declined from 28.7 percent (27.8 percent of the total female population, 28.4 percent of the total male population, 75 percent of the total juvenile population) during the Bronze and Iron Ages, to 15.5 percent during the Hunnu (2209–1907 BP) period, the rate of females with cribra orbitalia remained roughly the same, while the incidence of cribra orbitalia among males and children declined (29.4 percent of the total female population, 5.3 percent of the total male population, and 25 percent of the juvenile population had cribra orbitalia). Bazarsad posits several reasons for this distribution of cribra orbitalia: adults may have lower rates of cribra orbitalia than juveniles because lesions either heal with age or lead to death. Higher rates of cribia orbitalia among females may indicate lesser health status, or greater survival of young females with cribia orbitalia into adulthood.
Harris lines form before adulthood, when bone growth is temporarily halted or slowed down due to some sort of stress (either disease or malnutrition). During this time, bone mineralization continues, but growth does not, or does so at very reduced levels. If and when the stressor is overcome, bone growth will resume, resulting in a line of increased mineral density that will be visible in a radiograph. If there is not recovery from the stressor, no line will be formed.
The stress hormone cortisol is deposited in hair as it grows. This has been used successfully to detect fluctuating levels of stress in the later lifespan of mummies.
Examining the effects that activities and workload has upon the skeleton allows the archaeologist to examine who was doing what kinds of labor, and how activities were structured within society. The division of labor within the household may be divided according to gender and age, or be based on other hierarchical social structures. Human remains can allow archaeologists to uncover patterns in the division of labor.
Living bones are subject to Wolff's law, which states that bones are physically affected and remodeled by physical activity or inactivity. Increases in mechanical stress tend to produce bones that are thicker and stronger. Disruptions in homeostasis caused by nutritional deficiency or disease or profound inactivity/disuse/disability can lead to bone loss. While the acquisition of bipedal locomotion and body mass appear to determine the size and shape of children's bones, activity during the adolescent growth period seems to exert a greater influence on the size and shape of adult bones than exercise later in life.
Muscle attachment sites (also called entheses) have been thought to be impacted in the same way causing what were once called musculoskeletal stress markers, but now widely named entheseal changes. These changes were widely used to study activity-patterns, but research has shown that processes associated with aging have a greater impact than occupational stresses. It has also been shown that geometric changes to bone structure (described above) and entheseal changes differ in their underlying cause with the latter poorly affected by occupation. Joint changes, including osteoarthritis, have also been used to infer occupations but in general these are also manifestations of the aging process.
Markers of occupational stress, which include morphological changes to the skeleton and dentition as well as joint changes at specific locations have also been widely used to infer specific (rather than general) activities. Such markers are often based on single cases described in clinical literature in the late nineteenth century. One such marker has been found to be a reliable indicator of lifestyle: the external auditory exostosis also called surfer's ear, which is a small bony protuberance in the ear canal which occurs in those working in proximity to cold water.
One example of how these changes have been used to study activities is the New York African Burial Ground in New York. This provides evidence of the brutal working conditions under which the enslaved labored; osteoarthritis of the vertebrae was very common, even among the young. The pattern of osteoarthritis combined with the early age of onset provides evidence of labor that resulted in mechanical strain to the neck. One male skeleton shows stress lesions at 37 percent of 33 muscle or ligament attachments, showing he experienced significant musculoskeletal stress. Overall, the interred show signs of significant musculoskeletal stress and heavy workloads, although workload and activities varied among different individuals. Some individuals show high levels of stress, while others do not. This references the variety of types of labor (e.g., domestic vs. carrying heavy loads) labor that enslaved individuals were forced to perform.
Fractures to bones during or after excavation will appear relatively fresh, with broken surfaces appearing white and unweathered. Distinguishing between fractures around the time of death and post-depositional fractures in bone is difficult, as both types of fractures will show signs of weathering. Unless evidence of bone healing or other factors are present, researchers may choose to regard all weathered fractures as post-depositional.
Evidence of perimortal fractures (or fractures inflicted on a fresh corpse) can be distinguished in unhealed metal blade injuries to the bones. Living or freshly dead bones are somewhat resilient, so metal blade injuries to bone will generate a linear cut with relatively clean edges rather than irregular shattering. Archaeologists have tried using the microscopic parallel scratch marks on cut bones in order to estimate the trajectory of the blade that caused the injury.
Dental caries, commonly referred to as cavities or tooth decay, are caused by localized destruction of tooth enamel, as a result of acids produced by bacteria feeding upon and fermenting carbohydrates in the mouth. Subsistence based upon agriculture is strongly associated with a higher rate of caries than subsistence based upon foraging, because of the higher levels of carbohydrates in diets based upon agriculture. For example, bioarchaeologists have used caries in skeletons to correlate a diet of rice and agriculture with the disease. Females may be more vulnerable to caries compared to men, due to lower saliva flow than males, the positive correlation of estrogens with increased caries rates, and because of physiological changes associated with pregnancy, such as suppression of the immune system and a possible concomitant decrease in antimicrobial activity in the oral cavity.
Stable isotope analysis of carbon and nitrogen in human bone collagen allows bioarchaeologists to carry out dietary reconstruction and to make nutritional inferences. These chemical signatures reflect long-term dietary patterns, rather than a single meal or feast. Stable isotope analysis monitors the ratio of carbon 13 to carbon 12 (13C/12C), which is expressed as parts per mil (per thousand) using delta notation (δ13C). The ratio of carbon isotopes varies according to the types of plants consumed with different photosynthesis pathways. The three photosynthesis pathways are C3 carbon fixation, C4 carbon fixation and Crassulacean acid metabolism. C4 plants are mainly grasses from tropical and subtropical regions, and are adapted to higher levels of radiation than C3 plants. Corn, millet and sugar cane are some well-known C4 domesticates, while all trees and shrubs use the C3 pathway. C3 plants are more common and numerous than C4 plants. Both types of plants occur in tropical areas, but only C3 plants occur naturally in colder areas. 12C and 13C occur in a ratio of approximately 98.9 to 1.1.
The 13C and 12C ratio is either depleted (more negative) or enriched (more positive) relative to the international standard, which is set to an arbitrary zero. The different photosynthesis pathways used by C3 and C4 plants cause them to discriminate differently towards 13C The C4 and C3 plants have distinctly different ranges of 13C; C4 plants range between -9 and -16 per mil, and C3 plants range between -22 to -34 per mil. δ13C studies have been used in North America to document the transition from a C3 to a C4 (native North American plants to corn) diet. The rapid and dramatic increase in 13C after the adoption of maize agriculture attests to the change in the southeastern American diet by 1300 CE.
Isotope ratios in food, especially plant food, are directly and predictably reflected in bone chemistry, allowing researchers to partially reconstruct recent diet using stable isotopes as tracers. 
Nitrogen isotopes (14N and 15N) have been used to estimate the relative contributions of legumes verses nonlegumes, as well as terrestrial versus marine resources to the diet. 
The increased consumption of legumes, or animals that eat them, causes 15N in the body to decrease. Nitrogen isotopes in bone collagen are ultimately derived from dietary protein, while carbon can be contributed by protein, carbohydrate, or fat in the diet. Compared to other plants, legumes have lower 14N/15N ratios because they can fix molecular nitrogen, rather than having to rely on nitrates and nitrites in the soil. Legumes have δ15N values close to 0%, while other plants, which have δ15N values that range from 2 to 6%. Nitrogen isotope ratios can be used to index the importance of animal protein in the diet. 15N increases about 3-4% with each trophic step upward. 15N values increase with meat consumption, and decrease with legume consumption. The 14N/15N ratio could be used to gauge the contribution of meat and legumes to the diet.
Skeletons excavated from the Coburn Street Burial Ground (1750 to 1827 CE) in Cape Town, South Africa, were analyzed using stable isotope data by Cox et al. in order to determine geographical histories and life histories of the interred. The people buried in this cemetery were assumed to be slaves and members of the underclass based on the informal nature of the cemetery; biomechanical stress analysis and stable isotope analysis, combined with other archaeological data, seem to support this supposition.
Based on stable isotope levels, eight Cobern Street Burial Ground individuals consumed a diet based on C4 (tropical) plants in childhood, then consumed more C3 plants, which were more common at the Cape later in their lives. Six of these individuals had dental modifications similar to those carried out by peoples inhabiting tropical areas known to be targeted by slavers who brought enslaved individuals from other parts of Africa to the colony. Based on this evidence, Cox et al. argue that these individuals represent enslaved persons from areas of Africa where C4 plants are consumed and who were brought to the Cape as laborers. Cox et al. do not assign these individuals to a specific ethnicity, but do point out that similar dental modifications are carried out by the Makua, Yao, and Marav peoples. Four individuals were buried with no grave goods, in accordance with Muslim tradition, facing Signal Hill, which is a point of significance for local Muslims. Their isotopic signatures indicate that they grew up in a temperate environment consuming mostly C3 plants, but some C4 plants. Many of the isotopic signatures of interred individuals indicate that they Cox et al. argue that these individuals were from the Indian Ocean area. They also suggest that these individuals were Muslims. Cox et al. argue that stable isotopic analysis of burials, combined with historical and archaeological data can be an effective way in of investigating the worldwide migrations forced by the African Slave Trade, as well as the emergence of the underclass and working class in the colonial Old World.
Stable isotope analysis of strontium and oxygen can also be carried out. The amounts of these isotopes vary in different geological locations. Because bone is a dynamic tissue that is remodeled over time, and because different parts of the skeleton are laid down at particular times over the course of a human life, stable isotope analysis can be used to investigate population movements in the past and indicate where people lived at various points of their lives.
aDNA analysis of past populations is used by archaeology to genetically determine the sex of individuals, determine genetic relatedness, understand marriage patterns, and investigate prehistoric population movements.
An example of Archaeologists using DNA to find evidence, in 2012 archaeologists found skeletal remains of an adult male. He was buried under a car park in England. with the use of DNA evidence, the archaeologists were able to confirm that the remains belonged to Richard III, the former king of England who died in the Battle of Bosworth.
In 2021, Canadian researchers used DNA analysis on skeletal remains found on King William Island, identifying them as belonging to Warrant Officer John Gregory, an engineer serving aboard HMS Erebus in the ill-fated 1845 Franklin Expedition. He was the first expedition member to be identified by DNA analysis.
Aspects of the relationship between the physical body and socio-cultural conditions and practices can be recognized through the study of human remains. This is most often emphasized in a "biocultural bioarchaeology" model. It has often been the case that bioarchaeology has been regarded as a positivist, science-based discipline, while theories of the living body in the social sciences have been viewed as constructivist in nature. Physical anthropology and bioarchaeology have been criticized for having little to no concern for culture or history. Blakey has argued that scientific or forensic treatments of human remains from archaeological sites construct a view of the past that is neither cultural nor historic, and has suggested that a biocultural version of bioarchaeology will be able to construct a more meaningful and nuanced history that is more relevant to modern populations, especially descent populations. By biocultural, Blakey means a type of bioarchaeology that is not simply descriptive, but combines the standard forensic techniques of describing stature, sex and age with investigations of demography and epidemiology in order to verify or critique socioeconomic conditions experienced by human communities of the past. The incorporation of analysis regarding the grave goods interred with individuals may further the understanding of the daily activities experienced in life.
Currently, some bioarchaeologists are coming to view the discipline as lying at a crucial interface between the science and the humanities; as the human body is non-static, and is constantly being made and re-made by both biological and cultural factors.
Buikstra considers her work to be aligned with Blakey's biocultural version of bioarchaeology because of her emphasis on models stemming from critical theory and political economy. She acknowledges that scholars such as Larsen are productive, but points out that his is a different type of bioarchaeology that focuses on quality of life, lifestyle, behavior, biological relatedness, and population history. It does not closely link skeletal remains to their archaeological context, and is best viewed as a "skeletal biology of the past."
Inequalities exist in all human societies, even so-called “egalitarian” ones. It is important to note that bioarchaeology has helped to dispel the idea that life for foragers of the past was “nasty, brutish and short”; bioarchaeological studies have shown that foragers of the past were often quite healthy, while agricultural societies tend to have increased incidence of malnutrition and disease. However, based on a comparison of foragers from Oakhurst to agriculturalists from K2 and Mapungubwe, Steyn believes that agriculturalists from K2 and Mapungubwe were not subject to the lower nutritional levels expected for this type of subsistence system.
Danforth argues that more “complex” state-level societies display greater health differences between elites and the rest of society, with elites having the advantage, and that this disparity increases as societies become more unequal. Some status differences in society do not necessarily mean radically different nutritional levels; Powell did not find evidence of great nutritional differences between elites and commoners, but did find lower rates of anemia among elites in Moundville.
An area of increasing interest among bioarchaeologists interested in understanding inequality is the study of violence. Researchers analyzing traumatic injuries on human remains have shown that a person's social status and gender can have a significant impact on their exposure to violence. There are numerous researchers studying violence, exploring a range of different types of violent behavior among past human societies. Including intimate partner violence, child abuse, institutional abuse, torture, warfare, human sacrifice, and structural violence.
There are ethical issues with bioarchaeology that revolve around treatment and respect for the dead. Large-scale skeletal collections were first amassed in the US in the 19th century, largely from the remains of Native Americans. No permission was ever granted from surviving family for study and display. Recently, federal laws such as NAGPRA (Native American Graves Protection and Repatriation Act) have allowed Native Americans to regain control over the skeletal remains of their ancestors and associated artifacts in order to reassert their cultural identities.
NAGPRA passed in 1990. At this time, many archaeologists underestimated the public perception of archaeologists as non-productive members of society and grave robbers. Concerns about occasional mistreatment of Native American remains are not unfounded: in a Minnesota excavation 1971, White and Native American remains were treated differently; remains of White people were reburied, while remains of Native American people were placed in cardboard boxes and placed in a natural history museum. Blakey relates the growth in African American bioarchaeology to NAGPRA and its effect of cutting physical anthropologist off from their study of Native American remains.
Bioarchaeology in Europe is not as affected by these repatriation issues as American bioarchaeology but regardless the ethical considerations associated with working with human remains are, and should, be considered. However, because much of European archaeology has been focused on classical roots, artifacts and art have been overemphasized and Roman and post-Roman skeletal remains were nearly completely neglected until the 1980s. Prehistoric archaeology in Europe is a different story, as biological remains began to be analyzed earlier than in classical archaeology.