[2] Shakhtar Donetsk were the defending champions, but were eliminated by eventual finalists Fulham in the round of 32.

Associations were allocated places according to their 2008 UEFA country coefficient, which took into account their performance in European competitions from 2003–04 to 2007–08.

As this was the first edition of the Europa League, it was initially unknown whether UEFA would simply disregard the vacant title holder spot and rearrange entries so that one more team would qualify from the play-off round, or replace the title holders' group stage place with that of the top-ranked association's cup winner and move teams from lower rounds appropriately, as the regulations were unclear on this matter.

When a place was vacated, it was redistributed within the national association by the following rules:[4] The labels in the parentheses show how each team qualified for the place of its starting round:[6] All draws held at UEFA headquarters in Nyon, Switzerland unless stated otherwise.

[7] In the qualifying phase and the play-off round, teams played against each other over two legs on a home-and-away basis.

Both the first and second legs between Bnei Yehuda and Dinaburg and between Rapid Wien and Vllaznia were under investigation by UEFA and German authorities for possible match-fixing.

This was the first time teams from Latvia or Moldova qualified for the group stage of any European competition.

If two or more teams are equal on points on completion of the group matches, the following criteria are applied to determine the rankings:[4] During this stage of the tournament, matches featured five on-field officials – with two additional officials monitoring play around the penalty area as part of a FIFA-sanctioned experiment.

In the knockout phase, teams played against each other over two legs on a home-and-away basis, except for the one-match final.