Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/2009 |  | Stylianos Giannakopoulos | MF |  | Hull City | Hull City |
| 01/2009 |  | Saša Ilić | MF |  | RB Salzburg | RB Salzburg |
| 01/2009 |  | Tümer Metin | MF |  | Fenerbahçe | Fenerbahçe |
| 01/2009 |  | Milton Müller | MF | |||
| 10/2008 |  | Franck Guela | FW | |||
| 08/2008 |  | Laurent Robert | MF |  | Toronto FC | Toronto FC |
| 08/2008 | | Anastasios Kyriakos | MF |  | Asteras Tripolis | Asteras |
| 07/2008 | | Petros Baimakis | GK | |||
| 07/2008 |  | Dino Seremet | GK | |||
| 07/2008 |  | Tomislav Vranjić | GK |  | NK Inter Zaprešić | Zaprešić |
| 07/2008 |  | Naïm Aarab | DF |  | N.E.C. | N.E.C. |
| 07/2008 | | Mauricio Ferrari | DF |  | Ben Hur de Rafaela | Ben Hur |
| 07/2008 |  | Christian Weber | DF |  | MSV Duisburg | Duisburg |
| 07/2008 | | Dimitrios Balis | MF |  | Diagoras FC | Diagoras FC |
| 07/2008 | | Konstantinos Banousis | MF | |||
| 07/2008 |  | Nolberto Solano | MF |  | West Ham United | West Ham |
| 07/2008 | | Nikos Vlasopoulos | MF | |||
| 07/2008 |  | Mbo Mpenza | FW |  | RSC Anderlecht | Anderlecht |
| 07/2008 | | Athanasios Tsigas | FW |  | Atromitos | Atromitos |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/2009 | | Nolberto Solano | MF |  | Universitario de Deportes | Universitario |
| 01/2009 | | Konstantinos Banousis | MF |  | AO Chaidari | AO Chaidari |
| 01/2009 | | Andreas Labropoulos | MF |  | Panachaiki GE | Panachaiki GE |
| 01/2009 | | Alexandros Vergonis | MF |  | Olympiakos Volou | Olymp. Volou |
| 08/2008 |  | Nektarios Alexandrou | FW |  | APOEL Nikosia | APOEL |
| 07/2008 | | Spyros Christopoulos | GK |  | Thrasyvoulos Fylis | Thrasyvoulos Fylis |
| 07/2008 | | Fotis Kipouros | GK |  | Panserraikos | Panserraikos |
| 07/2008 | | Marco Förster | DF |  | Pafos FC | Pafos FC |
| 07/2008 | | Anastasios Venetis | DF |  | OFI Heraklion | OFI |
| 07/2008 | | Panagiotis Bachramis | MF |  | Veria FC | Veria FC |
| 07/2008 |  | Cleyton | MF |  | Panathinaikos A.O. | Panathinaikos |
| 07/2008 | | Georgios Galitsios | MF |  | Olympiacos FC | Olympiacos FC |
| 07/2008 | | Tümer Metin | MF | | Fenerbahçe | Fenerbahçe |
| 07/2008 | | Ibrahima Bakayoko | FW |  | PAOK Saloniki | PAOK |
| 07/2008 |  | Jozef Kožlej | FW | | Thrasyvoulos Fylis | Thrasyvoulos Fylis |
| 07/2008 | | Georgios Donis | MA |  | AEK Athen | AEK Athen |