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| Transfers |
 Inter 12,000,000 < >  Blackburn Rovers |
| GGA | > | Edon ZHEGROVA | RW/AM | KOS | 64 | 97 | 31/03/99 (26) | 90 | 1.81 | 70 | Blackburn Rovers | 7.09 | 17880 | | | | 1 | 0 | 4600 | 5 | +2 | |
| KQK | < | Calvin STENGS | AM/RW | NED | 62 | 93 | 18/12/98 (26) | 90 | 1.87 | 68 | Inter | 7.04 | 11960 | | | | 5 | 0 | 3440 | 7 | +1 | |
| WBR | > | Naif AGUERD | CB | MAR | 65 | 97 | 30/03/96 (29) | 86 | 1.88 | 73 | Blackburn Rovers | 6.89 | 20900 | | | | 3 | 0 | 2975 | 3 | +2 | |
| SDA | < | Leif DAVIS | LB/CB | ENG | 61 | 95 | 12/01/00 (25) | 90 | | | Inter | 6.70 | 10520 | | | | 2 | 0 | 2145 | 0 | +1 | |
Genoa 5,000,000 < >  1.FC Union Berlin |
| WZN | > | Bafodé DIAKITÉ | CB | FRA | 64 | 92 | 06/01/01 (24) | 90 | 1.82 | 74 | 1.FC Union Berlin | 6.60 | 18380 | | | | 6 | 0 | 3490 | 0 | +2 | |
 Real Sociedad 4,000,000 < > 1.FC Union Berlin |
| HIY | > | Johan Felipe VÁSQUEZ Ibarra | CB | MEX | 63 | 94 | 22/10/98 (26) | 94 | 1.82 | 72 | 1.FC Union Berlin | 6.43 | 14540 | | | | 8 | 0 | 2705 | 0 | +2 | |
 Panathinaikos < >  Rangers |
| YXS | < | Hamza IGAMANE | St | MAR | 62 | 92 | 21/05/01 (24) | 87 | 1.81 | 77 | Rangers | 6.38 | 11660 | | | | 1 | 0 | 4490 | 0 | +1 | (t.9, Panathinaikos) |
 Al-Ain < > SC Heerenveen |
| CMS | < | Matías SOULÉ Malvano | RW/AM | ARG | 63 | 91 | 15/04/03 (22) | 82 | 1.76 | 71 | SC Heerenveen | 7.08 | 11560 | | | | 2 | 0 | 5580 | 0 | +1 | (t.3, Al-Ain) |
AEK 10,250,000 < >  Club Brugge |
| RSN | > | Christos TZOLIS | LW | GRE | 63 | 95 | 30/01/02 (23) | 92 | 1.74 | 68 | Club Brugge | 6.63 | 16040 | | | | 3 | 1 | 5015 | 5 | +4 | |
| WBA < > 3,170,000 Newcastle United |
| VYV | < | Nick POPE | Gk | ENG | 66 | 12 | 19/04/92 (33) | 94 | 1.90 | 75 | WBA | | | | | | | | 2710 | | | |
| Coventry City < > 4,220,000 Lyon |
| JAY | < | Tammy ABRAHAM | CS | ENG | 63 | 0 | 02/10/97 (28) | 90 | 1.90 | 72 | Coventry City | | | | | | | | 4360 | | | |
| Juventus 6,560,000 < > Lyon |
| JYX | > | João Maria Lobo Alves PALHINHA Gonçalves | DM | POR | 65 | 97 | 09/07/95 (30) | 91 | 1.89 | 77 | Lyon | 6.87 | 21900 | | | | 6 | 0 | 2770 | 2 | +4 | |
| União Leiria 7,660,000 < > Lyon |
| BMG | > | Ismaïla SARR | AM/WS | SEN | 64 | 83 | 25/02/98 (27) | 95 | 1.80 | 70 | Lyon | | 19880 | | | | 0 | 0 | 4330 | 2 | +4 | |
 FC Nordsjælland 8,000,000 < > Feyenoord |
| YLB | > | Conrad HARDER | CS | DEN | 61 | 71 | 07/04/05 (20) | 90 | 1.81 | 71 | Feyenoord | | 11420 | | | | 0 | 0 | 5885 | 0 | +2 | |
| Leganés 2,000,000 < > Feyenoord |
| BOS | > | Yan DIOMANDE | W | CIV | 51 | 88 | 14/11/06 (18) | 83 | 1.80 | 75 | Feyenoord | | 1190 | | | | 0 | 0 | 1400 | 0 | Y | |
| Espanyol < > 660,000 Real Betis |
| LDX | < | Daniel Martín Fernández, DANI MARTÍN | Gk | ESP | 54 | 94 | 08/07/98 (27) | 93 | 1.86 | 76 | Espanyol | | 3390 | | | | 2 | 0 | 700 | 0 | +1 | |
| Leixões < > 3,300,000 Deportivo |
| VIM | < | YOUSSEF Ramalho CHERMITI | St | POR | 58 | 12 | 24/05/04 (21) | 83 | 1.92 | 81 | Leixões | | | | | | | | 3475 | | | |
| 800,000 < > Hamburger SV |
| PFZ | > | Diego KOCHEN | Gk | USA | 47 | 82 | 19/03/06 (19) | 89 | 1.88 | 80 | Hamburger SV | | 570 | | | | 0 | 0 | 505 | 0 | Y | |
 Adelaide United 4,750,000 < > Hamburger SV |
| PJZ | > | Nestory IRANKUNDA | W | AUS | 58 | 68 | 09/02/06 (19) | 86 | 1.75 | 74 | Hamburger SV | | 3350 | | | | 0 | 0 | 3560 | 1 | Y | |
 Daejon Citizen 1,250,000 < > Hamburger SV |
| WCS | > | YOON Do-young | RW/AM | KOR | 48 | 86 | 28/10/06 (18) | 92 | 1.73 | 66 | Hamburger SV | | 720 | | | | 0 | 0 | 905 | 0 | Y | |
| 1,400,000 < > Rayo Vallecano |
| KEB | > | ALYSSON EDWARD Franco da Rocha dos Santos | RW | BRA | 54 | 97 | 05/05/06 (19) | 93 | 1.75 | 59 | Rayo Vallecano | | 1760 | | | | 0 | 0 | 1995 | 0 | Y | |
| 505,000 < > Rayo Vallecano |
| MYR | > | Maher Mauricio CARRIZO | St | ARG | 44 | 86 | 19/02/06 (19) | 92 | 1.80 | 82 | Rayo Vallecano | | 380 | | | | 0 | 0 | 530 | 0 | Y | |
| 700,000 < > Rayo Vallecano |
| FRL | > | MARC Hidalgo DOMÈNECH | CS | ESP | 48 | 74 | 01/12/06 (18) | 91 | 1.82 | 70 | Rayo Vallecano | | 700 | | | | 0 | 0 | 1055 | 0 | Y | |
Dijon < > 520,000  IFK Göteborg |
| HHM | < | Mohamed EL AROUCH | CM | FRA | 46 | 2 | 06/04/04 (21) | 82 | 1.66 | 56 | Dijon | | | | | | | | 490 | | | |
 Vissel Kobe < > 1,220,000 FC Schalke 04 |
| UPR | < | Soichiro KOZUKI | RW | JPN | 54 | 15 | 22/12/00 (24) | 91 | 1.80 | 70 | Vissel Kobe | | | | | | | | 1170 | | | |
| Liverpool 9,000,000 < > FC Schalke 04 |
| QOT | > | Takefusa KUBO | W/AM | JPN | 65 | 46 | 04/06/01 (24) | 89 | 1.67 | 60 | FC Schalke 04 | 6.70 | 22000 | 6 | | | 15 | 2 | 5940 | 5 | +4 | |
| Borussia Dortmund 2,500,000 < > FC Schalke 04 |
| OME | > | Hiroki ITO | CB/LB | JPN | 63 | 94 | 12/05/99 (26) | 90 | 1.88 | 80 | FC Schalke 04 | 7.26 | 13340 | | | | 2 | 0 | 2705 | 9 | +4 | |
| PUS | < | Rabbi MATONDO | W | WAL | 56 | 88 | 09/09/00 (25) | 90 | 1.75 | 66 | Borussia Dortmund | 6.00 | 4810 | | | | 0 | 0 | 1500 | 0 | +1 | |
| 622,000 < > FC Utrecht |
| MZX | > | Denzel HALL | RB/CB | NED | 56 | 97 | 22/05/01 (24) | 92 | 1.80 | 74 | FC Utrecht | | 4650 | | | | 0 | 0 | 1075 | 0 | +1 | |
| 2,500,000 < > FC Utrecht |
| HQD | > | JHONATAN dos Santos Rosa | CM | BRA | 60 | 77 | 09/09/02 (23) | 92 | | | FC Utrecht | | 8000 | | | | 0 | 0 | 3245 | 0 | +1 | |
| 1,660,000 < > FC Utrecht |
| XJD | > | Marouan AZARKAN | LW | NED | 59 | 97 | 08/12/01 (23) | 92 | 1.65 | 63 | FC Utrecht | | 7150 | | | | 0 | 0 | 2805 | 0 | +1 | |
| 3,000,000 < > Ajax |
| VTD | > | Kevin Santos Lopes de Macedo, KEVIN MACEDO | St | BRA | 60 | 78 | 04/01/03 (22) | 88 | 1.80 | 70 | Ajax | | 9220 | | | | 0 | 0 | 4215 | 0 | +1 | |
| 1,000,000 < > Ajax |
| NXB | > | Ali MAAMAR | LB | BEL | 56 | 83 | 23/03/05 (20) | 90 | 1.85 | 75 | Ajax | | 5030 | | | | 0 | 0 | 1665 | 0 | +1 | |
| Released |
| QLC | 16 | Edgar 'Paul' AKOUOKOU | DM | CIV | 54 | 3 | 20/12/97 (27) | 85 | 1.88 | 62 | Nancy | | | 1 | | | | | 645 | | | |
| Loan callbacks |
| WMQ | 25+ | Nelson WEIPER | St | GER | 56 | 94 | 17/03/05 (20) | 88 | 1.92 | 81 | Milan | 5.96 | 2120 | | | | 2 | 1 | 2850 | 1 | Y | |
| GSU | - | Kevin SCHADE | St | GER | 63 | 95 | 27/11/01 (23) | 89 | 1.83 | 74 | Kaiserslautern | | 10820 | | | | 0 | 0 | 5850 | 0 | +2 | |
| EUQ | - | Sverre Halseth NYPAN | CM | NOR | 49/60 | 95 | 19/12/06 (18) | 61 | | | SC Heerenveen | 7.00 | 1800 | | | | 0 | 0 | 5130 | 1 | Y | |
| DFT | - | Caoimhin KELLEHER | Gk | IRL | 60/63 | 94 | 23/11/98 (26) | 75 | 1.88 | 75 | IFK Göteborg | | 9280 | | | | 0 | 0 | 2985 | 0 | +2 | |
| KDW | - | GABRIEL Silva MOSCARDO de Salles | DM | BRA | 58/59 | 78 | 28/09/05 (20) | 79 | | | Arsenal | | 4190 | | | | 0 | 0 | 2570 | 0 | Y | |
