The 1964–65 Intertoto Cup was won by Polonia Bytom, losing finalists the previous season, who defeated Lokomotive Leipzig in the final - believed to be the first held over two legs in the tournament's history. A total of 44 clubs participated, down four on the previous season, and clubs from Bulgaria and Greece took part for the first time. The competition was also affected by the decision of UEFA to prevent clubs who were taking part in the European Cup or UEFA Cup Winners' Cup continuing games in other European competitions after the end of the summer break. These clubs had to be given byes through the knock-out rounds until they were eliminated from the UEFA competitions, or withdrawn entirely.

Group stage

The teams were divided into eleven groups of four clubs each, it proving impossible to secure enough club to fill twelve groups. The groups were divided geographically - 'A' for Belgium, the Netherlands, Switzerland and West Germany; 'B' for Austria, Bulgaria, Czechoslovakia, East Germany, Poland, Yugoslavia and one club from Sweden; while 'C' (which had only 3 groups) was for France, Greece and Sweden, as well as one club each from Czechoslovakia, Poland and West Germany, and two from Yugoslavia, to make up the numbers. The eleven group winners (shown in bold in the tables below) advanced to the knock-out rounds.

Group A1

Group A2

Group A3

Group A4

Group B1

Group B2

Group B3

Group B4

Group C1

Group C2

Group C3

First round

Quarter-finals

Semi-finals

Final