Susan Blatchford, 11, and her 12-year-old friend Gary Hanlon vanished from their homes in north London in March 1970.
Their bodies were found months later in a copse and the newspapers at the time called them the "Babes in the wood".
Open verdict
The coroners' jury returned an open verdict, but their parents and the police are convinced they were murdered.
A Scotland Yard spokeswoman confirmed that a team of officers had dug up Susan's body under cover of darkness last week.
"There was a forensic examination and no arrests have been made," she said.
On the day they disappeared Susan had called round at Gary's home in Enfield and had asked him to go for a walk. When they failed to return 600 police officers searched the area.
Three months later, their bodies were found in Epping Forest, six miles from their homes.
New tests
Because of the length of time they had lain there, no forensic evidence was available.
However, the exhumation of Susan's body suggests that police scientists want to test a specific theory.
Three years ago, the investigation was re-opened by detectives looking into the possibilty that one or more paedophiles might have been involved.
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