| 1. Round | 18/09/2008 | Hamburger SV | - | FC Unirea | 0:0 | ||||
| 1. Round | 02/10/2008 | FC Unirea | - | Hamburger SV | 0:2 | ||||
| Group F | 23/10/2008 | MŠK Žilina | - | Hamburger SV | 1:2 | ||||
| Group F | 27/11/2008 | Hamburger SV | - | AFC Ajax | 0:1 | ||||
| Group F | 04/12/2008 | Slavia Praha | - | Hamburger SV | 0:2 | ||||
| Group F | 17/12/2008 | Hamburger SV | - | Aston Villa | 3:1 | ||||
| 3. Round | 18/02/2009 | NEC Nijmegen | - | Hamburger SV | 0:3 | ||||
| 3. Round | 26/02/2009 | Hamburger SV | - | NEC Nijmegen | 1:0 | ||||
| Round of 16 | 12/03/2009 | Hamburger SV | - | Galatasaray | 1:1 |  |
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| Round of 16 | 19/03/2009 | Galatasaray | - | Hamburger SV | 2:3 | ||||
| Quarter-finals | 09/04/2009 | Hamburger SV | - | Manchester City | 3:1 | ||||
| Quarter-finals | 16/04/2009 | Manchester City | - | Hamburger SV | 2:1 | ||||
| Semi-finals | 30/04/2009 | Werder Bremen | - | Hamburger SV | 0:1 | ||||
| Semi-finals | 07/05/2009 | Hamburger SV | - | Werder Bremen | 2:3 | |
Czech Republic