Ante Gotovina, 52, Ivan Cermak, 58, and Mladen Markac, 52, are accused of destroying towns and villages, killing over 150 Serb civilians and expelling about 200,000 others, in a 1995 operation conducted by the Croatian army in the Serbian Krajina region and led by Gotovina.
Prosecutor Alan Tieger said the three generals were involved in the attack on Krajina in the summer of 1995 aimed at ousting the Serb population for good.
Charges against Gotovina were brought in 2001, and against Cermak and Markac in 2004.
Gotovina used false names to evade justice for four years before being eventually tracked down and arrested in Spain in late 2005. The other two handed themselves in to the tribunal. All three have pleaded not guilty.
The indictment accused other high-ranking Croats, including former president Franjo Tudjman, Croatia's ex-defense minister and two army chiefs, of involvement in the crimes, but all four have since died.
