Workers at the trendy Manhattan restaurant, Freemans, were forced to hand over stool samples to the Department of Health — after a pregnant customer reported she contracted a food-borne illness at the eatery, The Post has learned.

The Lower East Side brunch hot-spot — which boasts celebrity clients and hour-long waits — was investigated for an outbreak of norovirus, a Department of Health spokesman said.

During the probe, workers were asked to do their business in a cup to prove they were free of the virus, which causes vomiting and diarrhea sources said.

“They came and checked everything yesterday…They tested everyone… [They took] stool samples,” a worker told The Post with a sheepish grin on Thursday.

The virus is contracted through fecal matter and person-to-person contact and effects roughly 20 million people every year.

“The Health Department was contacted about a possible food borne illness outbreak at Freeman’s. We suspect it is norovirus… The restaurant is cooperating while we continue our investigation,” a Department of Health and Mental Hygiene spokesman said.

Devoted regulars were quick to defend the eatery on Friday, saying it’s not a reflection of the restaurant’s quality.

“If you’re eating in an alley way or you’re eating on top of the Empire State Building, you’re going to have problems with food,” one customer said.

Another added, “Just because the Health department is doing an investigation doesn’t mean there’s a real issue here.”

The restaurant serves crème fraîche waffles for $12 and five-cheese macaroni for $15.

It’s favorite of actresses Mary Kate and Ashley Olsen.

A spokesman for the restaurant claimed the health department found no sign of norovirus.

“The Dept of Health did look into this at Freemans and have concluded their findings and ended their investigation and found no link or transmission of any kind at the restaurant,” said restaurant rep Eden Grimaldi.

“Freemans remains open, with an A rating,” Grimaldi added.

Stool testing restaurant workers is rare in New York but routine in norovirus cases, The Post has learned.

The restaurant serves “rustic” American cuisine, according to its Website.

Additional reporting by Ross Toback