Karadzic, who was arrested on a Belgrade bus in July 2008, 13 years after he was first indicted by the ICTY, is charged over his role in Bosnia's 1992-1995 war.
The main allegations against the 63-year-old relate to the 44-month siege of Sarajevo that left 10,000 dead, and the July 1995 massacre of around 8,000 Muslim men and boys in Srebrenica.
Among other counts, the prosecution has charged Karadzic with having sought to "permanently remove" Bosnian Muslims and Croats from Serb-claimed territory, and of aiming to "eliminate" Bosnian Muslims in Srebrenica.
He also stands accused of taking UN personnel hostage to prevent air strikes against Bosnian Serb military targets.
Karadzic repeated his claim on Tuesday that an agreement in 1996 with Richard Holbrooke, the US diplomat, had given him immunity from prosecution.
He said: "I am challenging the jurisdiction of this tribunal ... on the basis of my agreement with the international community whose representative at that point in time was Mr Richard Holbrooke."