Ian Huntley's hair was discovered on the Soham girls' clothes after police found them in a bin at their school, a court has been told.
Ian Huntley and Maxine Carr sat in the dock with a policeman between
The find was made on Friday 16 August, nearly two weeks after Holly Wells and Jessica Chapman disappeared, the prosecution claimed at the Old Bailey.
All of the girls' clothes had been cut off their bodies and an attempt had been made to burn them, prosecuting counsel Richard Latham QC said.
Mr Huntley, the 29-year-old former school caretaker, denies killing the 10-year-old girls, who went missing in the Cambridgeshire town on 4 August last year.
Mr Latham said police found the clothes after discovering keys to a "hangar", used for storage at the school, while searching Mr Huntley and Maxine Carr's home.
Using these keys they searched the hangar and in one of a number of yellow aluminium bins found the girls' clothing, including their trainers and underwear.
Mr Latham also said there was importance in the discovery of Mr Huntley's fingerprints on the inside of a bin bag where the clothes were found.
Mr Huntley missed the last section of the proceedings on Thursday, with his lawyer revealing he was not feeling well.
Earlier in the day, the prosecution said Mr Huntley behaved like a guilty man calmly "calculating his way forward" after the girls vanished, and had tried to throw police off the scent.
Mr Huntley thoroughly cleaned his car and replaced its tyres the day after the girls disappeared, the prosecution told the court.
The court was told that Mr Huntley had fitted new tyres to his car on the Monday afternoon, with the prosecution saying the mechanic who had fitted them had been given £10 by the car's owner to record a false registration number.
When they later searched the car, police found that a piece of domestic carpet "cut to make a rough fit" had replaced the carpet in the boot, the court heard.
The prosecution also said that on the Wednesday after the girls' disappearance, Mr Huntley had told police that in the previous few weeks a red Ford Fiesta had been seen in the area in suspicious circumstances.
Mr Latham suggested Huntley was trying to introduce a second car, knowing that a red Ford Fiesta was implicated in the case.
He said police visiting Mr Huntley's house noticed the ground floor was "immaculately tidy and there
was a strong smell of lemony cleaning product".
They also saw washing on the line, even though it was
pouring with rain.
The court heard that three days after the disappearance, Mr Huntley had asked officers involved in the search how long DNA could last and how far out of Soham the search would go.
The prosecution said Mr Huntley had asked a BBC journalist on the Thursday morning "have they found the girls' clothes?".
This meant he had to be the killer, the prosecution suggested, as it was not known the clothes had been separated from the bodies as neither had been found.
Tearful phone call
The court was told how on the Wednesday after the disappearance, the officer in charge of the investigation announced he had left a message for the abductor on Jessica's mobile.
At a public meeting the next day, Mr Huntley approached a senior officer and asked "how would the abductor get at the message if the battery was dead or it had been thrown away?".
Mr Latham also said Mr Huntley made a tearful phone call to his girlfriend Maxine Carr the morning after the 10-year-olds went missing.
Ms Carr denies charges of assisting an offender and conspiracy to pervert the course of justice.
The prosecution said Mr Huntley told Ms Carr: "I am going to get fitted up like I did before."
Later in the week, the pair were interviewed by police as part of the house-to-house inquiries, and gave an account about seeing the girls on the day they disappeared with Mr Huntley talking to them outside the house, and Ms Carr being inside in the bath.
The families are attending the trial
The prosecution reminded the jury that Ms Carr was in Grimsby at the time the pair were referring to.
Mr Huntley had told police on Monday night he had seen a man carrying something substantial running towards the woods in Soham. This was a lie, Mr Latham said.
Mr Latham added that Mr Huntley's actions often followed telephone calls with Ms Carr, who was in Grimsby.
Ms Carr, 26, has denied two charges of assisting an offender and one of conspiring to pervert the course of justice.
Mr Huntley denies two counts of murder but has admitted a single charge of conspiring to pervert the course of justice.
The case was adjourned until Friday.