Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 02/2009 |  | Sebastian Schindzielorz | MF |  | VfL Wolfsburg II | Wolfsburg II |
| 01/2009 |  | Peter Pekarík | DF |  | MŠK Žilina | Žilina |
| 01/2009 |  | Yoshito Okubo | FW | |||
| 09/2008 |  | Marwin Hitz | GK |  | FC St. Gallen II | St. Gallen II |
| 09/2008 | | Bernd Korzynietz | DF |  | Arminia Bielefeld | Bielefeld |
| 08/2008 |  | Caiuby | FW |  | São Caetano - SP | São Caetano |
| 07/2008 | | Patrick Platins | GK |  | FC Augsburg | Augsburg |
| 07/2008 |  | Andrea Barzagli | DF |  | Palermo FC | Palermo |
| 07/2008 | | Rodrigo Alvim | DF |  | Os Belenenses | Belenenses |
| 07/2008 | | Cristian Zaccardo | DF | | Palermo FC | Palermo |
| 07/2008 | | Daniel Adlung | MF |  | SpVgg Greuther Fürth | Gr. Fürth |
| 07/2008 |  | Zvjezdan Misimović | MF |  | 1. FC Nuremberg | Nuremberg |
| 07/2008 |  | Vlad Munteanu | MF |  | AJ Auxerre | Auxerre |
| 07/2008 | | Kevin Wolze | MF |  | Bolton Wanderers U18 | U18 |
| 07/2008 |  | Isaac Boakye | FW |  | 1. FSV Mainz 05 | Mainz 05 |
| 07/2008 | | Alexander Esswein | FW |  | 1. FC Kaiserslautern | K'lautern |
| 07/2008 | | Sergiu Radu | FW |  | VfB Stuttgart | Stuttgart |
| 07/2008 |  | Mahir Sağlık | FW |  | Wuppertaler SV | Wuppertal |
| 07/2008 | | Michele Putaro | RE-C |  | SSV Vorsfelde | Vorsfelde |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 02/2009 |  | Jacek Krzynówek | MF |  | Hannover 96 | Hannover |
| 02/2009 |  | Jonathan Santana | MF |  | San Lorenzo | CASL |
| 02/2009 | | Mahir Sağlık | FW |  | Karlsruher SC | Karlsruhe |
| 01/2009 | | Bernd Korzynietz | DF |  | MSV Duisburg | Duisburg |
| 01/2009 | | Jonas Deumeland | GK |  | Rot-Weiß Oberhausen | Oberhausen |
| 01/2009 | | Vlad Munteanu | MF | | Arminia Bielefeld | Bielefeld |
| 09/2008 | | Daniel Baier | MF | | FC Augsburg | Augsburg |
| 09/2008 | | Alexander Laas | MF | | Arminia Bielefeld | Bielefeld |
| 08/2008 |  | Mame Niang | FW |  | Viking FK | Viking |
| 08/2008 | | Isaac Boakye | FW | | 1. FC Nuremberg | Nuremberg |
| 08/2008 | | Marcelinho Paraíba | MF |  | Flamengo RJ | Flamengo |
| 08/2008 | | Sergiu Radu | FW |  | 1. FC Köln | Köln |
| 07/2008 | | Simon Jentzsch | GK | | VfL Wolfsburg II | Wolfsburg II |
| 07/2008 |  | Facundo Quiroga | DF |  | River Plate | River Plate |
| 07/2008 |  | Peter Van Der Heyden | DF | | 1. FSV Mainz 05 | Mainz 05 |
| 07/2008 |  | Alex | MF | | VfL Wolfsburg II | Wolfsburg II |
| 07/2008 |  | Cédric Makiadi | MF | | MSV Duisburg | Duisburg |
| 07/2008 |  | Valdet Rama | MF |  | FC Ingolstadt 04 | Ingolstadt |
| 07/2008 |  | Danijel Ljuboja | FW | | VfB Stuttgart | Stuttgart |
| 07/2008 | | Emre Öztürk | FW |  | SV Sandhausen | Sandhausen |