The group stage of the 2008–09 UEFA Cup is the second stage of the competition proper.^[1] The draw took place on 7 October 2008 at UEFA headquarters in Nyon, Switzerland.^[2] Group stage matches began on 23 October 2008 and concluded on 18 December 2008.^[3] The top three teams in each group progressed to the Round of 32, to be joined by the eight third-place finishers from the Champions League group stage.^[4]

The following teams qualified for the group stage:^[5]

More information Team, Coef. ...

Team	Coef.	Team	Coef.	Team	Coef.
Pot 1		Pot 2		Pot 3
Milan	119.934	Stuttgart	52.078	Rosenborg	35.400
Sevilla	102.837	Ajax	51.610	Udinese	34.934
Valencia	83.837	Olympiacos	51.525	Feyenoord	33.610
Benfica	77.176	Deportivo La Coruña	46.837	Braga	33.176
Schalke 04	67.078	Club Brugge	41.810	Slavia Prague	31.496
CSKA Moscow	59.437	Spartak Moscow	40.437	Manchester City	30.996
Tottenham Hotspur	55.996	Paris Saint-Germain	37.380	Galatasaray	30.469
Hamburg	52.078	Heerenveen	35.610	Sampdoria	28.934
Pot 4		Pot 5
Hertha BSC	27.078	Saint-Étienne	17.380
Partizan	25.527	Wolfsburg	16.078
Nancy	25.380	Standard Liège	14.810
Portsmouth	24.996	Twente	14.610
Aston Villa	24.996	NEC	12.610
Racing Santander	24.837	Metalist Kharkiv	10.932
Copenhagen	23.748	Lech Poznań	6.973
Dinamo Zagreb	17.836	Žilina	4.070

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Pot 1 contained teams ranked between 2 and 39: Pot 2 held teams ranked 40 to 71, Pot 3 held teams ranked 72 to 88, and Pot 4 teams ranked 91 to 122 together with unranked teams from England and Spain.^[6] Pot 5 held the remaining teams.

Dinamo Zagreb, and all the Pot 5 teams, had beaten higher-ranked teams in the first round. Lech Poznań and Žilina had also beaten higher-ranked teams in the Second Qualifying Round. Seven of the eight teams in Pot 5 qualified for the Round of 32, Žilina being the only exception. In contrast, only five of the eight teams in Pot 1 managed to do the same, as Sevilla, Benfica and Schalke 04 were eliminated.

Based on paragraph 6.06 in the UEFA regulations for the current season, if two or more teams are equal on points on completion of the group matches, the following criteria are applied to determine the rankings:^[1]

1. superior goal difference from all group matches played;
2. higher number of goals scored;
3. higher number of goals scored away;
4. higher number of wins;
5. higher number of away wins;
6. higher number of coefficient points accumulated by the club in question, as well as its association, over the previous five seasons.