The charges against Gotovina include crimes against humanity and war crimes, allegedly committed during the 1995 operation he led to recapture parts of Croatia from Serb rebels.
The indictment was summarized by a court registrar, who said"the accused Ante Gotovina, acting individually and/or in concert with other members of the joint criminal enterprise, planned, instigated, ordered, committed or otherwise aided and abetted in the planning, preparation or execution of the persecution of the Krajina Serb population in the southern part of the Krajina region."
Gotovina was arrested on Spain's Canary Islands on 7 December after four years on the run. He was transferred to The Hague on 10 December.
Gotovina is the court's third-most-wanted man, after the former Bosnian Serb political and military leaders Radovan Karadzic and Ratko Mladic, both of whom remain at large.
Many Croats, however, consider Gotovina to be a war hero.
Thousands of people turned out in the Croatian city of Split on 11 December to take part in a rally called in support of Gotovina.