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Huntley was given two life sentences.
The two ten-year-old girls, who were best friends, vanished from a family barbecue at Holly's house in Soham, Cambridgeshire, on 4 August 2002.
Their bodies were found in a ditch nearly two weeks later after one of the biggest police operations the UK has ever seen.
As the verdicts came in, it emerged Huntley, 29, has been accused of having sex with underage girls and of rape several times in the past.
His girlfriend, Maxine Carr, 26, was sentenced to three and a half years in jail for conspiring to pervert the course of justice by giving a false alibi to police for Huntley on the day of the murder.
She was cleared of two counts of assisting an offender.
Carr has already spent 16 months in prison and is likely to be freed with an electronic tag in a few months' time.
Sentencing Huntley, Mr Justice Moses said he had displayed "merciless cynicism" after killing the 10-year-old girls.
The judge said: "You murdered them both. You are the one person who knows how you murdered them, you are the one person who knows why."
He also told Huntley that he had added to the families' grief by pretending to help search for the girls and by offering words of sympathy to Holly's father.
As the jury returned 11 to 1 majority verdicts on Huntley, the Wells family hugged each other and sobbed.
Huntley showed no emotion.
Jessica's father, Leslie Chapman, described Huntley as a "timebomb just ready to go off".
"Unfortunately our girls were in the wrong place at the wrong time," he said.
He said he hoped Huntley would one day have "the guts" to publicly explain what happened on the night the girls died.
Huntley was a school caretaker at the time of the murders. Maxine Carr was a teaching assistant in the girls' class.
In court, Huntley said that Holly died after falling into his bath, and he said he killed Jessica accidentally when he put his hand over her mouth to stop her screaming.
But the prosecution laid out an alternative version of events - that Huntley lured Holly and Jessica into his house, possibly with a sexual motivation, and murdered them when his plan went wrong.
Maxine Carr was released from prison in May 2004, her identity protected by a court injunction.
There was strong criticism of the way the police and media handled the investigation into the murders, and the Home Secretary, David Blunkett, ordered an inquiry.
The Bichard Inquiry's report was published in June 2004. It was a damning indictment of the two police forces, who, it said, failed to share evidence and deleted vital files, including an intelligence report which identified Huntley as a "serial sex attacker".
The main blame was laid on Humberside Police. The Home Secretary, David Blunkett, moved to suspend the Chief Constable of Humberside Police, David Westwood, but he refused to resign.
He was supported by his police authority in an unprecendented show of defiance to the Home Secretary.
However, they were forced to back down after Mr Blunkett took the matter to the High Court. Mr Westwood returned to work in September 2004 after agreeing to retire a year early, in March 2005.
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