They believe the fruit could even help to ward off heart disease and cancer.
Using gene technology they were able to increase levels of beneficial chemicals called falvonols in tomato peel.
Flavonols are powerful antioxidants, chemicals which fight disease by neutralising harmful oxygen molecules that circulate in the body, damaging tissues and accelerating the ageing process.
They are found naturally in tomato skin, but at much lower levels.
The British and Dutch scientists found that flavonol synthesis in the tomato is governed by an enzyme called chalcone isomerase.
Petunia
They discovered a gene found in the Petunia plant which stimulates production of this enzyme.
By inserting the gene into the skin of a tomato, they were able to increase flavonol production by up to 78 times.
Taste was not affected, and 65% of the flavonols were retained when the GM tomatoes were processed into paste.
One type of flavonol, quercetin glycoside, was "significantly increased" in the peel of the modified tomatoes.
Smaller but still substantial increases in another flavonol called kaempferol glysoside were also seen.
The scientists, led by Martine Verhoeyen, from Unilever Research at Sharnbrook, Bedfordshire, said the research could lead to "functional" tomato-based food products such as pizza.
"These new varieties may offer opportunities for tomato-based products with an expanded range of potential health benefit properties."
Plant chemicals
Sara Stanner, of the British Nutrition Foundation, said there was growing evidence that certain chemicals found in plants did have a beneficial impact on health.
She told BBC News Online: "There are clear benefits associated with this type of GM food, but also concerns about safety aspects.
"It is up to the individual choice of the consumer, and it is important that these foods are properly labelled so that people can make that choice."
Ms Stanner said that if people ate five portions of fresh fruit and vegetables a day, then they would derive significant health benefits - and there would be little need for functional foods.
However, she said: "Perhaps we are being a bit idealistic in believing that people are going to follow that advice."
The research is published in the journal Nature Biotechnology.