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| Transfers |
 Bayern München 350,000 < >  Leeds United |
| SOO | > | Aleksandar PAVLOVIC | DM | GER | 43 | 97 | 03/05/04 (19) | 87 | | | Leeds United | | 350 | | | | 0 | 0 | 235 | 0 | Y | |
 Lille 2,500,000 < > Leeds United |
| JFQ | > | Leny YORO | CB | FRA | 55 | 73 | 13/11/05 (18) | 88 | | | Leeds United | | 2280 | | | | 0 | 0 | 1700 | 0 | Y | |
 FC København 2,000,000 < > Leeds United |
| KRK | > | Roony BARDGHJI | W/CS | SWE | 51 | 89 | 15/11/05 (18) | 86 | | | Leeds United | | 1180 | | | | 0 | 0 | 1400 | 0 | Y | |
| FC København 6,500,000 < > Manchester United |
| XCI | > | Jonas Older WIND | AM/CS | DEN | 62 | 79 | 07/02/99 (24) | 90 | 1.86 | 76 | Manchester United | | 12360 | | | | 0 | 0 | 3855 | 2 | +1 | |
 Bodø/Glimt 5,200,000 < > Manchester United |
| QTM | > | Jens Petter HAUGE | W/CS | NOR | 61 | 94 | 12/10/99 (24) | 86 | 1.84 | 75 | Manchester United | | 9310 | | | | 0 | 0 | 3330 | 0 | +1 | |
| 475,000 < > Torquay United |
| UPZ | > | Allan TCHAPTCHET | CB | FRA | 51 | 97 | 21/12/01 (21) | 90 | | | Torquay United | | 1970 | | | | 0 | 0 | 710 | 0 | +1 | |
| 386,000 < > Torquay United |
| HBD | > | Bobby THOMAS | CB | ENG | 50 | 96 | 30/01/01 (22) | 98 | 1.86 | 77 | Torquay United | | 1590 | | | | 0 | 0 | 540 | 0 | +1 | |
| Sedan 920,000 < > Cambridge United |
| EZE | > | Wes BURNS | RWB | WAL | 55 | 94 | 23/11/94 (28) | 92 | 1.73 | 68 | Cambridge United | | 3440 | | | | 0 | 0 | 705 | 0 | +1 | |
 Cenral Coast 1,055,000 < > Burton Albion |
| DVS | > | Tom GLOVER | Gk | AUS | 54 | 70 | 24/12/97 (25) | 97 | 1.90 | 90 | Burton Albion | | 2970 | | | | 0 | 0 | 880 | 0 | +1 | |
 PEC Zwolle 1,235,000 < > Rushden&Diamonds |
| PNA | > | Yuta NAKAYAMA | CB/CM | JPN | 56 | 84 | 16/02/97 (26) | 90 | 1.80 | 70 | Rushden&Diamonds | | 3980 | | | | 0 | 0 | 950 | 0 | +1 | |
| Released |
| MKY | 16 | Tom CLEVERLEY | CM/AM | ENG | 58 | 14 | 12/08/89 (34) | 93 | 1.75 | 67 | NY Red Bulls | | | | | | | | 385 | | | |
| Loan callbacks |
| DXZ | - | Jordan HENDERSON | CM | ENG | 66 | 66 | 17/06/90 (33) | 93 | 1.82 | 67 | Liverpool | | 44240 | | | | 0 | 0 | 2430 | 0 | | |
