Infamous boxers Michael Mineo wore when cop allegedly sodomized him go missing from courthouse

An underwear thief may be on the loose in Brooklyn Federal Court.

The plaid boxer shorts tattoo artist Michael Mineo wore when a cop allegedly sodomized him with a baton have vanished.

Both sides in the civil retrial of NYPD cop Richard Kern, who is being sued for using excessive force against Mineo, claim the blood-stained skivvies are key evidence in the case.

Reluctant to call in the FBI to investigate, Federal Judge Jack Weinstein conducted an inquisition last Thursday, grilling court clerks and lawyers.

"We're nonplussed as to what happened," said Mineo's lawyer Steven Jackson, a transcript shows. "I've never been involved in a case where evidence disappeared."

The underwear had been stored in a sealed bag inside a sealed box, secured in the courthouse vault.

The box, which also contained Kern's expandable baton in a sealed bag and Mineo's jeans, was brought to Weinstein's courtroom Tuesday afternoon.

Jackson removed the baton for trial purposes, but did not take note of the undies. "I assumed everything was there," he told the judge.

After the baton was returned to the box, a member of the Internal Affairs Bureau took custody of the items and returned them Wednesday morning, the city's lawyer says.

"Who authorized you to remove it from the courthouse?" Weinstein thundered. "In the future, nothing is to be removed from this courthouse without the court's order."

No one is sure whether the boxer shorts were even in the box when it was brought to court, or if they were misplaced after the first civil trial, which ended in a hung jury against Kern earlier this year.

The civil jury cleared three other cops in the case.

Mineo's lawyers have accused IAB investigators of tampering with the shorts by removing a flap allegedly caused by the baton puncturing the fabric.

The city insists there was never a flap.

A textile expert testified at the first trial that the square hole in the underwear could not have been made by Kern's baton, suggesting Mineo might have made the hole himself with a tattoo needle.

Kern and two other cops were acquitted of criminal charges in February, and jurors said the underwear played a key role.