Parents have called for tests on restaurant furniture to be part of hygiene inspections after highchairs were found to be dirtier than tables.
Samples taken at Stoke-on-Trent restaurants by the BBC revealed bacteria on highchairs that could have been removed with "modest cleaning".
One mother said the results were "very worrying", though the bacteria found was not a health risk, experts said.
The Food Standards Agency said hygiene criteria did not cover such furniture.
Dr Andrew Morris, from Keele University, said some of the nine highchairs swabbed by the BBC had more than 12 times the amount of bacteria that would be expected on the day they were tested.
He labelled it "a failing in diligent cleaning".
Dr Morris said the level of bacteria found would not cause babies or children any health problems but it was a concern highchairs clearly were not being cleaned efficiently.
He raised particular concern about coliform bacteria, commonly associated with the digestive system, which was found on the highchairs as "you would expect even the most modest of cleaning would kill them [the bacteria] off quite effectively".
"The fact that we're still finding them implies this is not happening," he said.
"It's very worrying because of the age of the children," Stoke-on-Trent mum Jo Leighton said. "They're very vulnerable at that age."
"You wouldn't serve a meal on a dirty plate, so why make a child sit on a dirty seat?"
She said, like many parents, she wiped down highchairs before using them but said: "Obviously it's what we can't see that's the problem."
"We don't really carry the right facilities to [clean them] properly," she said.
Ms Leighton said she would like to see restaurants' hygiene ratings extended to include more than the food preparation areas.
Her opinion was echoed by Dr Morris who said it would be "perhaps helpful if guidance could be given".
The Food Standards Agency (FSA) said there were currently no hygiene criteria for restaurant furniture, and while the bacteria were not "inherently dangerous, [they] can suggest poor hygiene practices which should be addressed".
Supported by Keele University, the BBC took samples once each from a highchair and a table at Burger King, KFC and McDonald's outlets, branches of Costa, Caffè Nero and Starbucks, and cafes in Morrisons, Asda, and Tesco.
Tested highchairs at all of the outlets were found to be dirtier than tables, apart from at McDonald's, where they were cleaner, and the Tesco cafe, which had the same level of bacteria.
The Hanley Burger King was found to have the most bacteria on a highchair, followed by KFC in Hanley's Festival Park.
The BBC raised its findings with the companies and Burger King said it upheld a strict cleaning routine and staff were happy to oblige if a customer believed a surface to be "sub par".
A KFC spokesperson said it "isn't great" but it had "given our teams a refresher and all our highchairs a good clean".
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