During the 1999–2000 season, MSV Duisburg played in the 1. Bundesliga, the highest tier of the German football league system.

After 3 years of top-half finishes, Duisburg were relegated in last place.

Squad at end of season^[1]

No. Pos. Nation Player 2 DF  GER Thomas Hoersen 3 DF  GER Dietmar Hirsch 4 DF  GER Torsten Wohlert 5 DF  POL Tomasz Hajto 7 MF  GER Marijan Kovačević 8 MF  GER Markus Osthoff 10 FW  POL Piotr Reiss 11 DF  CZE Pavel Drsek 12 MF  GER Andreas Voss (on loan from Bayer Leverkusen) 13 FW  GER Markus Beierle 14 MF  GER Marcus Wedau 15 MF  GER Horst Steffen 16 MF  GER Martin Schneider 17 DF  GER Thorsten Schramm 18 FW  GER Uwe Spies

No. Pos. Nation Player 19 MF  GER Jörg Neun 20 MF  GER Michael Zeyer 21 MF  GER Thomas Vana 22 DF  GER Stefan Emmerling 23 MF  GER Ralf Keidel 24 DF  GER Carsten Wolters 25 GK  LTU Gintaras Staučė 26 GK  GER Carsten Krämer 27 DF  POL Peter Schyrba 28 DF  GER Alexander Bugera (on loan from Bayern Munich) 29 FW  TUR Sercan Güvenışık 30 GK  GER Andreas Menger 31 MF  PER Rainer Torres 32 MF  MAR Yasser El Hamrouni 33 MF  GER Mike Büskens

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply. Players may hold more than one non-FIFA nationality.

No. Pos. Nation Player 6 MF  DEN Stig Tøfting (on loan to AGF)

No. Pos. Nation Player 9 FW  DEN Erik Bo Andersen (on loan to Vejle Boldklub)