In total, 60 teams participated: 18 fromAlpha Ethniki, 18 fromBeta, and 24 fromGamma. The competition was held over six rounds, included the final. The first three rounds weresingle elimination matches.AEK Athens andPAOK, both of the Alpha Ethniki, were eliminated by lower division teamsPoseidon Michaniona andPanserraikos respectively. As is typically seen in this tournament, half of the eight quarter-final teams came from Beta Ethniki. They wereKalamata, Panserraikos,Athinaikos andILTEX Lykoi.
The final was contested inAthens atOlympic Stadium on 5 May 1999, bythe eternal enemies, Olympiacos and Panathinaikos. They had last met in the Greek Cup Final in1992–93. Panathinaikos had earlier eliminatedCup holders Panionios in the first round while Olympiacos had eliminated Ionikos by an impressive 4–7 score in the third round. Olympiacos won 2–0 and achieved their 20th Cup conquest.[1] With the victory, Olympiacos achieved theDouble for the first time in 18 years. With the Cup final loss, Panathinaikos became the first team to lose the Cup final three times in a row.[2]
Each tie in theknockout phase, apart from the first three rounds and the final, was played overtwo legs, with each team playing one leg at home. The team that scored more goals on aggregate over the two legs advanced to the next round. If the aggregate score was level, theaway goals rule was applied, i.e. the team that scored more goals away from home over the two legs advanced. If away goals were also equal, thenextra time was played. The away goals rule was again applied after extra time, i.e. if there were goals scored during extra time and the aggregate score was still level, the visiting team advanced by virtue of more away goals scored. If no goals were scored during extra time, the winners were decided by apenalty shoot-out. In the first three rounds and the final, which were played as a single match, if the score was level at the end of normal time, extra time was played, followed by a penalty shoot-out if the score was still level. The mechanism of the draws for each round is as follows:
There are no seedings, and teams from the same group can be drawn against each other.