The first round of the 2008–09 UEFA Cup began on 16 September 2008, which narrowed clubs down to 40 teams in preparation for the group stage.
32 teams entered the tournament at the first round, along with the 32 winners from the previous round and the 16 losers from the Champions League third qualifying round. The 80 teams were then split into eight groups of ten teams; five seeded teams and five unseeded teams. The draw was based on their coefficient ranking with one exception: no country can have multiple teams in any group. Teams ranked 108 or higher were seeded, as were unranked teams from England and Spain. The draw, which was conducted by UEFA General Secretary David Taylor, was held on 29 August 2008 at 13:00 CET in Monaco.
| Seeded teams | Group | Unseeded teams | ||||
|---|---|---|---|---|---|---|
| Rank | Team | Coefficient rating | Rank | Team | Coefficient rating | |
| 1 | 119.934 | 1 | 48 | 16.993 | ||
| 16 | 40.469 | 59 | 13.398 | |||
| 17 | 40.437 | 62 | 11.496 | |||
| 32 | 27.078 | 65 | 10.932 | |||
| 33 | 25.527 | 80 | 2.420 | |||
| 2 | 102.837 | 2 | 45 | 18.176 | ||
| 15 | 41.398 | 49 | 16.078 | |||
| 18 | 37.380 | 63 | 11.469 | |||
| 31 | 28.934 | 66 | 10.840 | |||
| 36 | 24.996 | 79 | 2.640 | |||
| 3 | 83.837 | 3 | 46 | 17.836 | ||
| 14 | 41.810 | 52 | 15.176 | |||
| 19 | 36.496 | 64 | 11.013 | |||
| 29 | 30.996 | 67 | 7.993 | |||
| 34 | 25.380 | 77 | 3.327 | |||
| 4 | 77.176 | 4 | 42 | 19.934 | ||
| 13 | 43.996 | 53 | 14.810 | |||
| 20 | 36.398 | 60 | 12.610 | |||
| 30 | 30.469 | 68 | 7.993 | |||
| 37 | 24.837 | 78 | 3.176 | |||
| 5 | 67.078 | 5 | 44 | 18.644 | ||
| 12 | 46.837 | 51 | 15.176 | |||
| 21 | 35.610 | 61 | 12.400 | |||
| 27 | 31.840 | 70 | 6.973 | |||
| 35 | 24.996 | 76 | 3.327 | |||
| 6 | 59.437 | 6 | 43 | 18.748 | ||
| 9 | 52.078 | 54 | 14.610 | |||
| 22 | 35.400 | 58 | 13.398 | |||
| 28 | 31.496 | 69 | 7.644 | |||
| 38 | 24.380 | 75 | 3.836 | |||
| 7 | 55.996 | 7 | 41 | 21.078 | ||
| 10 | 51.610 | 50 | 15.973 | |||
| 23 | 34.934 | 55 | 14.437 | |||
| 26 | 32.644 | 72 | 5.527 | |||
| 39 | 23.748 | 74 | 4.070 | |||
| 8 | 52.078 | 8 | 47 | 17.380 | ||
| 11 | 51.525 | 56 | 14.070 | |||
| 24 | 33.610 | 57 | 13.398 | |||
| 25 | 33.176 | 71 | 6.748 | |||
| 40 | 21.197 | 73 | 4.518 | |||
The matches were played on 18 September and 2 October 2008.
Nine of the 40 ties were won by the unseeded team. The nine seeded losing teams, with their ranking, were: Everton (50), Rapid București (58), Beşiktaş (60), Sparta Prague (68), Dinamo București (69), Levski Sofia (80), Austria Wien (82), Rennes (97) and Hapoel Tel Aviv (108).
|-!colspan="5"|Group 1|-!colspan="5"|Group 2|-!colspan="5"|Group 3|-!colspan="5"|Group 4|-!colspan="5"|Group 5|-!colspan="5"|Group 6|-!colspan="5"|Group 7|-!colspan="5"|Group 8|}
------------------------------------------------------------------------------------------------------------------------------------------------------------
Hertha BSC won 2–0 on aggregate.----Schalke 04 won 5–2 on aggregate.----Olympiacos won 7–0 on aggregate.----CSKA Moscow won 3–1 on aggregate.----Rosenborg won 5–3 on aggregate.----VfB Stuttgart won 4–3 on aggregate.----Rennes 2–2 Twente on aggregate. Twente won on away goals.----Ajax won 6–1 on aggregate.----Tottenham Hotspur won 3–2 on aggregate.----Copenhagen won 3–2 on aggregate.----MŠK Žilina won 2–1 on aggregate.----Borussia Dortmund 2–2 Udinese on aggregate. Udinese won 4–3 on penalties.----Braga won 6–0 on aggregate.----Feyenoord 2–2 Kalmar on aggregate. Feyenoord won on away goals.----Hamburger SV won 2–0 on aggregate.----Saint-Étienne won 4–2 on aggregate.----Milan won 4–1 on aggregate.----Partizan won 3–1 on aggregate.----Aston Villa won 4–2 on aggregate.----Lech Poznań won 5–4 on aggregate.----Heerenveen won 6–3 on aggregate.----Brann 2–2 Deportivo La Coruña on aggregate. Deportivo La Coruña won 3–2 on penalties.----Slavia Prague 1–1 Vaslui on aggregate. Slavia Prague won on away goals.----Spartak Moscow won 2–1 on aggregate.----Metalist Kharkiv won 4–2 on aggregate.----Portsmouth won 4–2 on aggregate.----Paris Saint-Germain won 2–1 on aggregate.----Sevilla won 4–0 on aggregate.----VfL Wolfsburg won 2–1 on aggregate.----Sampdoria won 7–1 on aggregate.----Valencia won 3–1 on aggregate.----Dinamo Zagreb 3–3 Sparta Prague on aggregate. Dinamo Zagreb won on away goals.----Manchester City won 4–2 on aggregate.----Club Brugge won 4–2 on aggregate.----Nancy won 3–0 on aggregate.----Standard Liège won 4–3 on aggregate.----Benfica won 4–3 on aggregate.----Galatasaray won 6–4 on aggregate.----NEC won 1–0 on aggregate.----Racing Santander won 2–0 on aggregate.