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The 1968–69 Greek Football Cup was the 27th edition of the Greek Football Cup. The competition culminated with the Greek Cup Final, held at Karaiskakis Stadium, on 9 July 1969. The match was contested by Panathinaikos and Olympiacos, with Panathinaikos winning on the toss of a coin, because of the final result (1–1).
In the knockout phase, teams play against each other over a single match. If the match ends up as a draw, extra time will be played. If a winner doesn't occur after the extra time the winner emerges by a flip of a coin. The mechanism of the draws for each round is as follows:
In the draw for the round of 32, the teams that had qualified to previous' season Round of 16 are seeded and the clubs that passed the qualification round are unseeded.
In the draws for the round of 16 onwards, there are no seedings, and teams from the same group can be drawn against each other.