Prosecutors at the United Nations war crimes tribunal in the Hague accused Tolimir of authorizing the 1995 massacres in the enclaves of Srebrenica and Zepa. There, the Bosnian army killed some 8,000 Muslim men and boys and forced tens of thousands of women and children from their homes.
Tolimir pleaded not guilty and plans to conduct his own defense.
The army general was a top aide to Ratko Mladic, the commander of Bosnian Serb forces. Mladic is the most wanted war criminal still at large from the Balkan wars.
Tolimir's case opened as the court ordered its biggest war crimes case to resume. The court rejected a motion by the wartime leader of the Bosnian Serbs, Radovan Karadzic, to postpone his trial until June. Karadzic will make his opening defense statements on March 1 and 2.
On Tuesday, Serbian police searched the Mladic home in suburban Belgrade (Banovo brdo) after sealing off the surrounding area.
The Serbian war crimes prosecutor (Vladimir Vukcevic) ordered the search as part of an ongoing effort to capture the war crimes suspect, sought by the United Nations war crimes tribunal in the Hague.
Serbian authorities have repeatedly searched the homes of top war crimes fugitives and their relatives in recent years, in efforts to dismantle their support network.
Mladic and other top Bosnian Serb leaders went into hiding following the 1995 Dayton peace accord that ended the ethnic conflict in Bosnia-Herzegovina.