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.
Seeding
Summary
First leg
| Hertha BSC  | 2–0 |  St Patrick's Athletic | 
|---|---|---|
| Nicu  50' Cícero  77' | Report | 
| APOEL  | 1–4 |  Schalke 04 | 
|---|---|---|
| Mirosavljević  72' | Report | Westermann  25' Rakitić  36' Sánchez  41' Altıntop  88' | 
| Nordsjælland  | 0–2 |  Olympiacos | 
|---|---|---|
| Report | Mitroglou  74' Leto  90+1' | 
| Slaven Belupo  | 1–2 |  CSKA Moscow | 
|---|---|---|
| Jurić  43' | Report | Vágner Love  81', 89' (pen.) | 
| Brøndby  | 1–2 |  Rosenborg | 
|---|---|---|
| Krohn-Dehli  63' | Sapara  29' Skjelbred  55' | 
| Cherno More  | 1–2 |  Stuttgart | 
|---|---|---|
| Dyakov  42' | Report | Gómez  66', 81' | 
| Borac Čačak .svg.png.webp) | 1–4 |  Ajax | 
|---|---|---|
| Milovanović  50' | Report | Sulejmani  11' Suárez  35' Huntelaar  71', 86' | 
| Tottenham Hotspur  | 2–1 |  Wisła Kraków | 
|---|---|---|
| Bentley  33' Bent  73' | Report | Jirsák  34' | 
| FC Moscow  | 1–2 |  Copenhagen | 
|---|---|---|
| Samedov  90+1' | Report | Nordstrand  45' (pen.) Sionko  90+3' | 
| MŠK Žilina  | 1–1 |  Levski Sofia | 
|---|---|---|
| Vladavić  49' (pen.) | Report | Joãozinho  64' | 
| Borussia Dortmund  | 0–2 |  Udinese | 
|---|---|---|
| Report | Floro Flores  8' Inler  34' | 
| Hapoel Tel Aviv  | 1–2 |  Saint-Étienne | 
|---|---|---|
| Lala  88' | Report | Payet  7' Feindouno  60' | 
| Litex Lovech  | 1–3 |  Aston Villa | 
|---|---|---|
| Popov  10' | Report | Reo-Coker  45+1' Barry  72' (pen.) Petrov  90+2' | 
| Austria Wien  | 2–1 |  Lech Poznań | 
|---|---|---|
| Schiemer  64', 76' | Report | Rengifo  65' | 
| Vitória de Setúbal  | 1–1 |  Heerenveen | 
|---|---|---|
| Leandro Carrijo  67' | Report | Elyounoussi  90' | 
| Baník Ostrava  | 0–1 |  Spartak Moscow | 
|---|---|---|
| Report | Fathi  56' | 
| Beşiktaş  | 1–0 |  Metalist Kharkiv | 
|---|---|---|
| Hološko  51' | Report | Report | 
| Portsmouth  | 2–0 |  Vitória de Guimarães | 
|---|---|---|
| Diarra  39' Defoe  60' | Report | 
| Kayserispor  | 1–2 |  Paris Saint-Germain | 
|---|---|---|
| Toledo  87' | Report | Kežman  5' Luyindula  89' | 
| Sevilla  | 2–0 |  Red Bull Salzburg | 
|---|---|---|
| Capel  6' Adriano  90+2' | Report | 
| Wolfsburg  | 1–0 |  Rapid București | 
|---|---|---|
| Grafite  47' (pen.) | Report | 
| Omonia  | 1–2 |  Manchester City | 
|---|---|---|
| Duro  49' | Report | Jô  59', 72' | 
| Young Boys .svg.png.webp) | 2–2 | .svg.png.webp) Club Brugge | 
|---|---|---|
| Schneuwly  16' Doumbia  87' | Report | Sonck  36' Clement  73' | 
| Nancy  | 1–0 |  Motherwell | 
|---|---|---|
| Berenguer  42' | Report | 
| Bellinzona .svg.png.webp) | 3–4 |  Galatasaray | 
|---|---|---|
| Lustrinelli  32' Sermeter  47' La Rocca  90' | Report | Kewell  39' Baroš  61', 81' Lincoln  90+5' | 
| N.E.C.  | 1–0 |  Dinamo București | 
|---|---|---|
| Van Beukering  57' | Report | 
| Racing Santander  | 1–0 |  Honka | 
|---|---|---|
| Pereira  57' | Report | 
Second leg
Hertha BSC won 2–0 on aggregate.
| Schalke 04  | 1–1 |  APOEL | 
|---|---|---|
| Pander  58' | Report | Pinto  6' | 
Schalke 04 won 5–2 on aggregate.
| Olympiacos  | 5–0 |  Nordsjælland | 
|---|---|---|
| Torosidis  11' Diogo  30', 43' Kovačević  72', 80' | Report | 
Olympiacos won 7–0 on aggregate.
| CSKA Moscow  | 1–0 |  Slaven Belupo | 
|---|---|---|
| A. Berezutski  37' | Report | 
CSKA Moscow won 3–1 on aggregate.
| Rosenborg  | 3–2 |  Brøndby | 
|---|---|---|
| Ya Konan  15' Skjelbred  74' Sapara  87' (pen.) | Report | M. Rasmussen  26' Kristiansen  36' | 
Rosenborg won 5–3 on aggregate.
| Stuttgart  | 2–2 |  Cherno More | 
|---|---|---|
| Hitzlsperger  83' Gómez  90+3' | report | Yurukov  48' Iliev  79' | 
Stuttgart won 4–3 on aggregate.
Rennes 2–2 Twente on aggregate. Twente won on away goals.
| Ajax  | 2–0 | .svg.png.webp) Borac Čačak | 
|---|---|---|
| Sarpong  71' Suárez  90+5' | Report | 
Ajax won 6–1 on aggregate.
| Wisła Kraków  | 1–1 |  Tottenham Hotspur | 
|---|---|---|
| Pa. Brożek  83' | Report | Głowacki  58' (o.g.) | 
Tottenham Hotspur won 3–2 on aggregate.
| Copenhagen  | 1–1 |  FC Moscow | 
|---|---|---|
| Sheshukov  54' (o.g.) | Report | Bracamonte  37' | 
Copenhagen won 3–2 on aggregate.
| Levski Sofia  | 0–1 |  MŠK Žilina | 
|---|---|---|
| Report | Adauto  61' | 
MŠK Žilina won 2–1 on aggregate.
| Udinese  | 0–2 (a.e.t.) |  Borussia Dortmund | 
|---|---|---|
| Report | Hajnal  45+1', 90+2' | |
| Penalties | ||
| Domizzi  Quagliarella  Pepe  Inler  Luković  | 4–3 |  Hajnal  Şahin  Kehl  Błaszczykowski  Valdez | 
Borussia Dortmund 2–2 Udinese on aggregate. Udinese won 4–3 on penalties.
| Artmedia Bratislava  | 0–2 |  Braga | 
|---|---|---|
| Report | Aguiar  11' (pen.), 31' | 
Braga won 6–0 on aggregate.
Feyenoord 2–2 Kalmar on aggregate. Feyenoord won on away goals.
| Unirea Urziceni  | 0–2 |  Hamburg | 
|---|---|---|
| Report | Petrić  27', 51' | 
Hamburg won 2–0 on aggregate.
| Saint-Étienne  | 2–1 |  Hapoel Tel Aviv | 
|---|---|---|
| Gomis  25', 76' | Report | Yeboah  90+1' | 
Saint-Étienne won 4–2 on aggregate.
| Zürich .svg.png.webp) | 0–1 |  Milan | 
|---|---|---|
| Report | Shevchenko  70' | 
Milan won 4–1 on aggregate.
| Partizan .svg.png.webp) | 1–0 |  Timișoara | 
|---|---|---|
| Stevanović  70' | Report | 
Partizan won 3–1 on aggregate.
| Aston Villa  | 1–1 |  Litex Lovech | 
|---|---|---|
| Harewood  27' | Report | Niflore  53' (pen.) | 
Aston Villa won 4–2 on aggregate.
| Lech Poznań  | 4–2 (a.e.t.) |  Austria Wien | 
|---|---|---|
| Rengifo  10' Peszko  85' Lewandowski  99' Murawski  120+1' | Report | Ačimovič  63' (pen.) Hattenberger  100' | 
Lech Poznań won 5–4 on aggregate.
| Heerenveen  | 5–2 |  Vitória de Setúbal | 
|---|---|---|
| Paulo Henrique  4' Sibon  11', 24' Elyounoussi  50', 68' | Report | Gama  57' Chaves  63' | 
Heerenveen won 6–3 on aggregate.
| Deportivo La Coruña  | 2–0 (a.e.t.) |  Brann | 
|---|---|---|
| Colotto  18', 76' | Report | |
| Penalties | ||
| Sergio  Mista  Guardado  Verdú  | 3–2 |  Bjarnson  Vaagan Moen  Bakke  Austin  Hanstveit | 
Brann 2–2 Deportivo La Coruña on aggregate. Deportivo La Coruña won 3–2 on penalties.
| Vaslui  | 1–1 |  Slavia Prague | 
|---|---|---|
| Burdujan  21' | Report | Brabec  48' | 
Slavia Prague 1–1 Vaslui on aggregate. Slavia Prague won on away goals.
| Spartak Moscow  | 1–1 |  Baník Ostrava | 
|---|---|---|
| Bazhenov  3' | Report | Otepka  32' | 
Spartak Moscow won 2–1 on aggregate.
| Metalist Kharkiv  | 4–1 |  Beşiktaş | 
|---|---|---|
| Jajá  20', 74' Dević  30' Gancarczyk  79' | Report | Nobre  90' | 
Metalist Kharkiv won 4–2 on aggregate.
| Vitória de Guimarães  | 2–2 (a.e.t.) |  Portsmouth | 
|---|---|---|
| Douglas  19' Alves  32' | Report | Crouch  105', 111' | 
Portsmouth won 4–2 on aggregate.
Paris Saint-Germain won 2–1 on aggregate.
| Red Bull Salzburg  | 0–2 |  Sevilla | 
|---|---|---|
| Report | Kanouté  38', 57' (pen.) | 
Sevilla won 4–0 on aggregate.
| Rapid București  | 1–1 |  Wolfsburg | 
|---|---|---|
| Maftei  70' | Report | Grafite  15' | 
Wolfsburg won 2–1 on aggregate.
Sampdoria won 7–1 on aggregate.
Valencia won 3–1 on aggregate.
| Sparta Prague  | 3–3 |  Dinamo Zagreb | 
|---|---|---|
| Kulič  19' Kladrubský  23', 82' (pen.) | Report | Morales  17' Lovren  30' Badelj  65' | 
Dinamo Zagreb 3–3 Sparta Prague on aggregate. Dinamo Zagreb won on away goals.
| Manchester City  | 2–1 |  Omonia | 
|---|---|---|
| Elano  48' Wright-Phillips  55' | Report | Alabi  78' | 
Manchester City won 4–2 on aggregate.
| Club Brugge .svg.png.webp) | 2–0 | .svg.png.webp) Young Boys | 
|---|---|---|
| Akpala  17' Sonck  29' | Report | 
Club Brugge won 4–2 on aggregate.
| Motherwell  | 0–2 |  Nancy | 
|---|---|---|
| Report | Fortuné  18' Gavanon  23' | 
Nancy won 3–0 on aggregate.
Standard Liège won 4–3 on aggregate.
| Benfica  | 2–0 |  Napoli | 
|---|---|---|
| Reyes  57' Nuno Gomes  84' | Report | 
Benfica won 4–3 on aggregate.
| Galatasaray  | 2–1 | .svg.png.webp) Bellinzona | 
|---|---|---|
| Baroš  24' (pen.) Yıldız  86' | Sermeter  52' (pen.) | 
Galatasaray won 6–4 on aggregate.
NEC won 1–0 on aggregate.
| Honka  | 0–1 |  Racing Santander | 
|---|---|---|
| Report | Bedia  4' | 
Racing Santander won 2–0 on aggregate.

