[3] This tournament was conducted under the UEFA Cup system having replaced at the 44th edition a standard knockout competition scheme.
The draw for the First Round was conducted at the headquarters of the TFF in Istanbul on 22 August 2008.
The draw for the Second Round was conducted at the headquarters of the TFF in Istanbul on 12 September 2008.
The four teams that finished first through fourth in 2007–08 Süper Lig were seeded as group heads: Galatasaray, Fenerbahçe, Beşiktaş and Sivasspor.
The sixteen teams qualified through the first two rounds of elimination matches were randomly drawn into one of the four groups.