Karr faces child pornography charges in Sonoma County, Calif. He was released to Sonoma sheriff's deputies, said Boulder County Sheriff's Lt. Phil West.
Karr, a schoolteacher, was arrested Aug. 16 in Thailand after he made phone calls and wrote e-mails in which he claimed to have killed the 6-year-old in her Boulder home in December 1996.
The case disintegrated when DNA tests showed Karr could not be the killer.
Five misdemeanor counts of child pornography possession have been pending against Karr in Sonoma since April 2001, when authorities arrested him and seized his computer, alleging that the hard drive contained five sexually oriented images of children.
Karr pleaded not guilty to all counts and was jailed for six months, but he left the country before he could be tried. Prosecutors decided to pursue the charges after Karr surfaced last month as a suspect in the JonBenet killing.
It was not immediately clear Tuesday when Karr would appear in court in California.
During preliminary hearings in 2001, Karr's public defenders waived his right to a speedy trial as they tried to get a judge to invalidate the search warrant that allowed Sonoma sheriff's deputies to enter Karr's home and seize his computer.