6 September 2008 : Bundesliga Transfers Updated| Player | Position | From | To | Fee €m | |
| Borowski | MF | Bremen | Bayern Munich | Free | |
| Butt | GK | Benfica | Bayern Munich | Free | |
| Klinsmann | Coach | Out of contract | Bayern Munich | n/a | |
| Bade | GK | Dortmund | Bielefeld | u/d | |
| Lamey | DF | Duisburg | Bielefeld | u/d | |
| Sadik | FW | Lahti | Bielefeld | u/d | |
| Fuchs | DF | Mattersburg | Bochum | u/d | |
| Huseinovic | MF | Sloboda Tuzla | Bremen | u/d | |
| Mertesacker | DF | Contract Extension | Bremen | 2012 | |
| Prodl | DF | Sturm Graz | Bremen | u/d | |
| Cadgas | DF | Trabzonspor | Cottbus | u/d | |
| Vragel | MF | Contract Extension | Cottbus | 2009 | |
| Klopp | Coach | Mainz | Dortmund | n/a | |
| Santana | DF | Figueirense | Dortmund | 2.00 | |
| Young Pyo | DF | PSV | Dortmund | u/d | |
| Bajramovic | MF | Schalke | Frankfurt | u/d | |
| Bellaid | DF | Strasbourg | Frankfurt | 2.50 | |
| Korkmaz | MF | Rapid Vienna | Frankfurt | u/d | |
| Liberoupolos | FW | AEK Athens | Frankfurt | u/d | |
| Jansen | DF | Bayern Munich | Hamburg | 8.00 | |
| Jol | Coach | Out of contract | Hamburg | n/a | |
| Chermiti | FW | Etoile du Sahel | Hertha Berlin | 2.00 | |
| Voronin | FW | Liverpool | Hertha Berlin | Loan | |
| Becker | Coach | Contract Extension | Karlsruher | 2010 | |
| Da Silva | MF | Stuttgart | Karlsruher | u/d | |
| Augusto | MF | Flamengo | Leverkusen | 5.00 | |
| Djakpa | DF | Pandurii Targu-Jiu | Leverkusen | 1.00 | |
| Henrique | DF | Barcelona | Leverkusen | Loan | |
| Kadlec | DF | Sparta Prague | Leverkusen | Loan | |
| Bradley | MF | Heerenveen | Moenchengladbach | 3.00 | |
| Jaures | DF | Auxerre | Moenchengladbach | Free | |
| Engelaar | MF | Twente | Schalke | 7.00 | |
| Boulahrouz | DF | Chelsea | Stuttgart | u/d | |
| Lehmann | GK | Out of contract | Stuttgart | Free | |
| Adlung | MF | Greuther Furth | Wolfsburg | u/d | |
| Alvim | DF | Belenenses | Wolfsburg | u/d | |
| Barzagli | DF | Palermo | Wolfsburg | 12.00 | |
| Misimovic | MF | Nurnberg | Wolfsburg | u/d | |
| Zaccardo | DF | Palermo | Wolfsburg | 7.00 | |
| 49.50 | |||||
| u/d = undisclosed | |||||