Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 08/2006 |  | Illiasu Shilla | DF |  | Asante Kotoko | Asante Kotoko |
| 07/2006 | | Baffour Gyan | FW |  | Dinamo Moskva | Din. Moskva |
| 07/2006 |  | Oleg Vlasov | MF |  | Zenit St. Petersburg | Zenit |
| 07/2006 |  | Dusan Petković | DF |  | OFK Beograd | OFK Beograd |
| 07/2006 | | Sergey Yashin | MF | | Dinamo Moskva | Din. Moskva |
| 07/2006 |  | Branislav Fodrek | FW |  | FC Petržalka | FC Petržalka |
| 06/2006 | | Igor Lebedenko | FW |  | Lokomotiv Moscow | Lok Moscow |
| 03/2006 | | Branislav Obžera | MF | | FC Petržalka | FC Petržalka |
| 02/2006 | | Peter Petráš | DF | | FC Petržalka | FC Petržalka |
| 02/2006 | | Vladimir Weiss | MA | | FC Petržalka | FC Petržalka |
| 01/2006 |  | Alexei Eremenko | MF |  | US Lecce | Lecce |
| 01/2006 | | Ján Ďurica | DF | | FC Petržalka | FC Petržalka |
| 01/2006 | | Vyacheslav Kalashnikov | DF | |||
| 01/2006 | | Ruslan Nakhushev | DF | |||
| 01/2006 | | Dmitriy Polovinchuk | DF | | Dinamo Moskva | Din. Moskva |
| 01/2006 | | Igor Shestakov | DF | |||
| 01/2006 |  | Luka Vučko | DF |  | Hajduk Split | Hajduk |
| 01/2006 |  | Edgaras Česnauskis | MF |  | Dynamo Kyiv | Dynamo Kyiv |
| 01/2006 |  | Simon Vukčević | MF |  | Partizan | Partizan |
| 01/2006 |  | Adriano | FW |  | Figueirense - SC | Figueirense |
| 01/2006 | | Spartak Gogniev | FW |  | Spartak Vladikavkaz | Spartak |
| 01/2006 | | Martin Jakubko | FW |  | Dukla Banská Bystrica | Bystrica |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 08/2006 | | Géder | DF |  | Spartak Moskva | Spartak |
| 07/2006 | | Luka Vučko | DF | | Hajduk Split | Hajduk |
| 07/2006 | | Aleksandr Kharitonov | MF |  | FK Khimki | FK Khimki |
| 07/2006 | | Adriano | FW |  | Denizlispor | Denizlispor |
| 07/2006 | | Spartak Gogniev | FW |  | FK Rostov | FK Rostov |
| 07/2006 | | Jean | FW |  | Vasco da Gama - RJ | Vasco da Gama |
| 07/2006 |  | Nicolás Pavlovich | FW |  | 1. FC Kaiserslautern | K'lautern |
| 01/2006 |  | Martín Hidalgo | DF |  | Libertad | Libertad |
| 01/2006 | | Diego Ianiero | DF |  | Argentinos Juniors | Arg. Juniors |
| 01/2006 | | Jean | DF | | Dinamo Moskva | Din. Moskva |
| 01/2006 | | Petr Bystrov | MF |  | FK Moskva | FK Moskva |
| 01/2006 |  | Javier Delgado | MF |  | Nacional | Nacional |
| 01/2006 | | Andrey Kanchelskis | MF |  | Krylia Sovetov | Krylia Sovetov |
| 01/2006 | | Aleksandr Makarenko | MF |  | Sibir Novosibirsk | FK Sibir |
| 01/2006 | | Roman Shirokov | MF |  | Rubin Kazan | Kazan |
| 01/2006 | | Aleksey Trinitatskiy | MF |  | Spartak Nalchik | Nalchik |
| 01/2006 | | Anton Arkhipov | FW | | FK Khimki | FK Khimki |
| 01/2006 |  | Winston Parks | FW | | Lokomotiv Moscow | Lok Moscow |
| 01/2006 |  | Serghei Rogaciov | FW |  | FK Aktobe | Aktobe |