The men surrendered to the UN tribunal in April 2004 and pleaded not guilty to charges including murder, rape, destruction of property and the deportation of Bosnian Muslims during the 1992-95 Bosnian conflict.
Prosecutor Kenneth Scott said in court that the men worked with Franjo Tudjman, the late Croatian president, who had long pursued plans for a "Greater Croatia", to include territory of Bosnia and Herzegovina.
Scott told the court that "Muslim majorities and pluralities did not stop Tudjman in claiming those areas".
The suspects were high-ranking military or political officials in a self-styled Bosnian Croat mini-state, including Jadranko Prlic, its then-prime minister, Bruno Stojic, the defence minister and Valentin Coric, the interior minister.
Two of the indictees, Slobodan Praljak and Milivoj Petkovic, were chiefs of the Bosnian Croat militia.
Charges relate to the murder of
The sixth suspect, Berislav Pusic, was a military police commander and in charge of prisons.
All have pleaded innocent to the 26 counts, which relate to the period 1991-1994.
The indictment charges them with responsibility for the cruel imprisonment of thousands of Muslims in military detention camps, where inmates were brutalised, beaten, underfed and kept in inhuman conditions.
Detainees were forced to beat others, including their own families. Some were shot.
If he had lived, Tudjman likely would have ranked just behind Serbian strongman Slobodan Milosevic as the tribunal's highest-profile case.
Milosevic died of a heart attack in prison last month, months before his four-year trial was to end.
Although Croatia recognised Bosnia-Herzegovina as an independent country in 1992, Tudjman ordered his troops to cross the border into the southeast of the country in 1993 on the pretext of protecting ethnic Croats.
The conflict had erupted in 1991 after Bosnian Serbs rebelled against Bosnia's secession from Yugoslavia and began grabbing territory in central Bosnia from Muslims and Croats in the hope of attaching it to the Serb Republic.
Tudjman's efforts mirrored those of Milosevic who, according to his indictment, was trying to create a greater Serbia.