Former European champions AC Milan, SL Benfica and FK Crvena Zvezda were among the initial entrants for the 2008/09 UEFA Cup along with past trophy winners Valencia CF, Sevilla FC and Tottenham Hotspur FC.

Competitors
In the last edition before the launch of the new UEFA Europa League and a 48-team group stage in 2009/10, 157 sides were in the running for FC Zenit St. Petersburg's title, including the last eleven UEFA Intertoto Cup winners and 24 entrants from the UEFA Champions League. Zenit themselves began in the senior competition but a third-place group finish meant they transferred to the UEFA Cup knockout phase. Even before their move there was a strong list of entants, starting from the first qualifying round when Manchester City FC, whose stadium was the venue for the 2007/08 final, were one of three Fair Play entrants.

Road to Istanbul
In all 74 teams went into the first qualifying round, drawn on 1 July and played later that month, with 27 sides including the last set of Intertoto winners joining at the next stage. The 32 second qualifying round winners joined 32 automatic entrants and the 16 teams eliminated in the UEFA Champions League third qualifying round in the first round, which produced the 40 group stage entrants. The top three in those pools moved into the knockout phase with the eight third-place UEFA Champions League teams, which included Zenit. The final will be played on 20 May at Istanbul's Şükrü Saracoğlu Stadium.

* domestic cup winners
** losing domestic cup finalists
*** domestic league cup winners
**** Fair Play winners
***** UEFA Intertoto Cup winners