Last month, Bonomy registered not guilty pleas to all the charges after Karadzic twice refused to enter one himself.
Karadzic intends to defend himself with the help of a team of legal advisers.
He is likely to use Wednesday's hearing to repeat his claim that he was promised immunity from prosecution in return for disappearing from the public eye in a 1996 deal with Richard Holbrooke, a US peace envoy, a claim Holbrooke has repeatedly denied.
Karadzic was arrested on a Belgrade bus in July after 13 years on the run.
At the time, he was disguised with white hair and a beard and working as a new age healer under the assumed name of Dr Dragan Dabic.
Bonomy had urged prosecutors to complete their drafting of a streamlined version of the indictment against Karadzic as soon as possible.
At an August 29 hearing, prosecutors said they hoped to be ready by the end
"I sincerely hope you are not serious about that date,'' Bonomy told Alan Tieger, a prosecutor.
The court is under pressure from the UN security council to complete its cases and close its doors by 2010.
Prosecutors have indicted 161 suspects on war crimes charges and convicted 57.
Two indicted suspects remain on the run, including General Ratko Mladic, Karadzic's military chief while he was in power, and Goran Hadzic, a former leader of Serbs in Croatia.