Pillay said human rights are "deteriorating" in Iran and that she is deeply concerned.
She also criticized Sri Lanka for failing to examine abuses committed during the government's war last year with Tamil Tiger rebels.
Pillay presented her 2009 report to the U.N. body Thursday.
She noted that the U.S. made some progress toward closing its prison at Guantanamo Bay. She urged Washington to thoroughly investigate torture allegations there and at the U.S.-run prison at Bagram Air Base in Afghanistan.