Kaing Geuk Eav, who is also known as Duch, wept as he led the investigating judges of the UN-assisted Khmer Rouge tribunal around the notorious S-21 prison.
He has been charged with crimes against humanity.
Spokesman for the tribunal, Reach Sambath, said Duch became emotional when shown a tree against which children were smashed to death.
"When he saw the tree trunk he said the children were smashed into the tree trunk," he said.
"At the end of the conversation he went on his leg and he, you know he pray, salute to the tree and he feel very emotioned."