In the 1979 Intertoto Cup no knock-out rounds were contested, and therefore no winner was declared.

Group stage

The teams were divided into eight groups of four teams each.

Group 1

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts
1	Werder Bremen	6	5	1	0	10	4	+6	11
2	Standard Liège	6	2	1	3	10	9	+1	5
3	Maccabi Netanya	6	1	2	3	8	10	−2	4
4	Rapid Wien	6	1	2	3	8	13	−5	4

Group 2

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts
1	Grasshopper	6	3	1	2	9	10	−1	7
2	Vejle	6	2	2	2	10	7	+3	6
3	Royal Antwerp	6	2	2	2	11	11	0	6
4	Duisburg	6	1	3	2	7	9	−2	5

Group 3

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts
1	Eintracht Braunschweig	6	4	2	0	15	7	+8	10
2	Malmö FF	6	4	1	1	13	9	+4	9
3	Slavia Prague	6	2	1	3	6	9	−3	5
4	St. Gallen	6	0	0	6	5	14	−9	0

Group 4

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts
1	Bohemians Prague	6	4	1	1	13	10	+3	9
2	IFK Göteborg	6	3	1	2	19	8	+11	7
3	Zürich	6	2	1	3	9	15	−6	5
4	Odense	6	1	1	4	10	18	−8	3

Group 5

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts
1	Spartak Trnava	6	4	2	0	9	3	+6	10
2	Esbjerg	6	3	1	2	12	8	+4	7
3	Kalmar	6	2	1	3	9	9	0	5
4	First Vienna	6	0	2	4	4	14	−10	2

Group 6

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts
1	Zbrojovka Brno	6	5	0	1	19	5	+14	10
2	Slavia Sofia	6	4	1	1	15	6	+9	9
3	Chênois	6	1	1	4	7	17	−10	3
4	LASK	6	1	0	5	4	17	−13	2

Group 7

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts
1	Pirin Blagoevgrad	6	4	0	2	9	6	+3	8
2	Katowice	6	2	3	1	5	4	+1	7
3	AGF	6	2	2	2	5	5	0	6
4	Casino Salzburg	6	0	3	3	4	8	−4	3

Group 8

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts
1	Baník Ostrava	6	4	1	1	14	9	+5	9
2	Öster	6	2	3	1	14	8	+6	7
3	Darmstadt	6	1	4	1	6	6	0	6
4	Grazer AK	6	0	2	4	7	18	−11	2