Jolie was accompanied to the museum by an entourage of seven people and her partner Brad Pitt.
Museum director Chey Sopheara said the visit lasted half an hour, saying: "I saw her with my own eyes. She bought tickets and toured the museum just like everybody else. It was a private visit."
Up to 16,000 prisoners were murdered at the prison, where the museum now stands, under Khmer Rouge rule during 1975-79; it is believed that only a handful of prisoners survived the mass bloodshed.
Jolie adopted her first child Maddox from Cambodia, she claims to have fallen in love with the country while she was filming �Tombraider� there several; years ago.
She and Pitt reportedly left Cambodia in a private plane last night; it is believed they have travelled back to India where Jolie is currently filming �A Mighty Heart�.
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