A Muslim man by the name of Hasanuddin is accused along with Lilik Purnomo and Irwanto Irano of killing the three girls as they walked to their private Christian school near their home in the town of Poso in central Sulawesi in October 2005. The killings were met with shock across Indonesia and the international Christian community.
Sulawesi has struggled to halt violence between the island's Muslims and Christians and the murders are believed to be religiously motivated, particularly as the head of one of the victims was left outside a church.
Tensions have threatened to boil over in recent weeks after three Christian militants were executed in September for fatal attacks against Muslims in 2000 - despite an appeal for clemency from the Pope and widespread international criticism of both the trial and sentences.
The suspects of the beheadings faces charges of premeditated murder and carrying out acts of terrorism, according to the BBC, and all three men could face the death sentence if they are found guilty.
The lawyer to the three men told the Associated Press before the trials that all three had confessed their involvement in the killings, which they said were to avenge Muslim deaths.
More than 1,000 people were killed between 1998 and 2001 during fierce sectarian fighting in Poso and nearby regions.
Sporadic violence continues despite a government-sponsored peace accord signed by Muslim and Christian leaders in the hope of securing lasting peace.