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.

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These clubs had to be given byes through the knock-out rounds until they were eliminated from the UEFA competitions, or withdrawn entirely.

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.