Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 05/2007 |  | Christos Bourbos | MF |  | AO Kerkyra | AO Kerkyra |
| 01/2007 | | Pantelis Kafes | MF | |||
| 07/2006 | | Ioannis Fysekis | GK | |||
| 07/2006 | | Savvas Gentsoglou | DF | |||
| 07/2006 | | Nikolaos Kourkoulas | DF | |||
| 07/2006 | | Sokratis Papastathopoulos | DF |  | Niki Volou FC | Niki Volou |
| 07/2006 |  | Martín Pautasso | DF |  | Independiente | Independiente |
| 07/2006 |  | Ifeanyi Udeze | DF |  | PAOK Saloniki | PAOK |
| 07/2006 | | Vasilios Vallianos | DF | |||
| 07/2006 |  | Përparim Hetemaj | MF |  | HJK Helsinki | HJK |
| 07/2006 | | Panagiotis Kone | MF | |||
| 07/2006 | | Panagiotis Lagos | MF |  | AEP Iraklis FC | Iraklis |
| 07/2006 | | Georgios Paligeorgos | MF | |||
| 07/2006 |  | Dániel Tőzsér | MF |  | Ferencvárosi TC | Ferencváros |
| 07/2006 | | Akis Zikos | MF |  | AS Monaco | AS Monaco |
| 07/2006 |  | Andrija Delibašić | FW |  | S.C. Braga | S.C. Braga |
| 07/2006 | | Leonidas Kampantais | FW |  | Panionios GSS | Panionios |
| 07/2006 |  | Manduca | FW |  | SL Benfica | Benfica |
| 07/2006 | | Michalis Pavlis | FW | |||
| 07/2006 |  | Serra Ferrer | MA |  | Real Betis | Betis |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/2007 | | Andrija Delibašić | FW |  | SC Beira-Mar | SC Beira-Mar |
| 01/2007 | | Miltos Sapanis | MF |  | APOEL Nikosia | APOEL |
| 01/2007 | | Vasilios Vallianos | DF |  | Anagennisi Karditsa | Anagennisi Karditsa |
| 07/2006 | | Christos Kontis | DF | | APOEL Nikosia | APOEL |
| 07/2006 |  | Nikola Malbasa | DF |  | TuS Koblenz | TuS Koblenz |
| 07/2006 | | Christos Bourbos | MF | | AO Kerkyra | AO Kerkyra |
| 07/2006 |  | Louay Chanko | MF |  | Hammarby IF | Hammarby |
| 07/2006 | | Kostas Katsouranis | MF | | SL Benfica | Benfica |
| 07/2006 | | Panagiotis Zorbas | MF | | Niki Volou FC | Niki Volou |
| 07/2006 |  | Oleg Venhlinskiy | FW |  | Chernomorets Odessa | Chernomorets |
| 07/2006 |  | Fernando Santos | MA | | SL Benfica | Benfica |
| 07/2006 | | Jorge Rosário | AS-CO | | SL Benfica | Benfica |
| 07/2006 | | Ricardo Santos | AS-CO | | SL Benfica | Benfica |