The LIX Legislature of the Congress of Guanajuato met from September 2003 to September 2006. All members of the Congress were elected in the 2003 Guanajuato state elections.
The LIX Legislature consisted of 36 deputies.
| Party | Deputies |
|---|---|
| National Action Party | 20 |
| Institutional Revolutionary Party | 9 |
| Party of the Democratic Revolution | 3 |
| Ecologist Green Party of Mexico | 2 |
| Labor Party | 1 |
| Independent | 1 |