"Not guilty on any of the counts," replied each of the six, who surrendered to the tribunal on Monday, after the 26 counts against them were read out.
The defendants include Jadranko Prlic and Bruno Stojic, respectively the former prime minister and defence minister of the statelet of Herceg-Bosna, which tried to secede from Bosnia after it broke away from Yugoslavia in 1992.
"I was not the master of war as I have been made out to be in the indictment," Prlic told presiding judge Alphons Orie.
Later the former prime-minister of the self-proclaimed statelet asked to make a statement.
"I sympathise with Bosnia-Hercegovina and all the victims mentioned in the indictment," said Prlic, adding he believed the truth would set him free.
The other suspects did not make a statement.
The UN court has charged Prlic and Stojic, Bosnian Croat generals Slobodan Praljak and Milivoj Petkovic, former military police commander Valentin Coric and the head of a prisoner exchange commission Berislav Pusic, with forming a joint criminal enterprise to "permanently remove or ethnically cleanse Bosnian Muslims and other non Croats" from parts of southwestern Bosnia to form a "Greater Croatia".
Retired Croatian General
Slobodan Praljak was also indicted
Bosnian Croats and Muslims were allies against ethnic Serbs during most of the war, but they turned on each other for 11 months in 1993-1994.
The campaign of "ethnic cleansing" included persecutions, deportations and illegal imprisonment of civilians, according to the indictment.
Praljak, 59, is specifically charged with ordering the destruction of the historic 16th-century bridge in the divided Bosnian town of Mostar in November 1993.
In court Pralak appeared weakened, hunched over and walking with crutches. He told the judge he had undergone spinal surgery last week.