Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 11/2008 |  | Dušan Bajević | MA | |||
| 09/2008 |  | Rafik Djebbour | FW |  | Panionios GSS | Panionios |
| 08/2008 |  | Agustín Pelletieri | MF |  | Lanús | Lanús |
| 08/2008 |  | Sotirios Kyrgiakos | DF | |||
| 08/2008 | | Angelos Basinas | MF |  | RCD Mallorca | Mallorca |
| 07/2008 | | Sebastián Saja | GK |  | San Lorenzo | CASL |
| 07/2008 |  | Juanfran | DF |  | Real Zaragoza | Zaragoza |
| 07/2008 | | Dimitrios Koutromanos | DF | |||
| 07/2008 |  | Daniel Majstorović | DF |  | FC Basel 1893 | FC Basel |
| 07/2008 |  | Nathan Burns | MF |  | Adelaide United | Adelaide United |
| 07/2008 |  | El-Hadji Diouf | MF |  | Ilisiakos | Ilisiakos |
| 07/2008 |  | Përparim Hetemaj | MF |  | Apollon Kalamarias | Ap. Kalamarias |
| 07/2008 | | Antonis Rikka | MF |  | Xanthi FC | Xhanti FC |
| 07/2008 | | Ignacio Scocco | MF |  | Pumas UNAM | Pumas UNAM |
| 07/2008 | | Panagiotis Zorbas | MF | |||
| 07/2008 | | Georgios Donis | MA |  | AE Lárissa | AE Lárissa |
| 05/2008 | | Makis Angelinas | AS-CO | |||
| 02/2008 | | Nikos Kostenoglou | MA | |||
| 01/2008 |  | Mohamed Kallon | FW |  | Al Hilal | Al Hilal |
| 01/2008 |  | Edinho | FW |  | Vitória Setúbal | Vitória FC |
| 01/2008 | | Panagiotis Tachtsidis | MF |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 09/2008 |  | Rivaldo | FW |  | Bunyodkor PFK | Bunyodkor PFK |
| 08/2008 | | Panagiotis Kone | MF |  | AEP Iraklis FC | Iraklis |
| 07/2008 | | Sokratis Papastathopoulos | DF |  | Genoa CFC | Genoa CFC |
| 07/2008 | | Traianos Dellas | DF |  | Anorthosis Famagusta | Anorthosis |
| 07/2008 | | Moretto | GK |  | SL Benfica | Benfica |
| 07/2008 | | Rodolfo Arruabarrena | DF |  | Tigre | C. A. T. |
| 07/2008 | | Federico Azcárate | DF |  | Polideportivo Ejido | Polideportivo Ejido |
| 07/2008 | | Christos Bourbos | MF | | AEP Iraklis FC | Iraklis |
| 07/2008 |  | Georgios Tofas | MF |  | Anagennisi Karditsa | Anagennisi Karditsa |
| 07/2008 |  | Dániel Tőzsér | MF |  | KRC Genk | KRC Genk |
| 07/2008 | | Júlio César | FW |  | Rapid Bucureşti | R. Bucureşti |
| 07/2008 | | Mohamed Kallon | FW |  | Al Shabab Al Arabi | Al Shabab |
| 07/2008 | | Pantelis Kapetanos | FW |  | FCSB | FCSB |
| 07/2008 | | Nikos Liberopoulos | FW |  | Eintracht Frankfurt | E. Frankfurt |
| 07/2008 | | Manú | FW |  | CS Marítimo | CS Marítimo |
| 07/2008 | | Charis Pappas | FW | | Xanthi FC | Xhanti FC |
| 01/2008 | | El-Hadji Diouf | MF | | Ilisiakos | Ilisiakos |
| 01/2008 | | Përparim Hetemaj | MF | | Apollon Kalamarias | Ap. Kalamarias |