Tiny particles of up to nine different types of plastic were found in every sample investigated – with people from the UK and seven other countries taking part in the study.
Plastic in the gut could suppress the immune system and aid the transmission of toxins and harmful bugs or viruses, experts believe.
It confirms fears raised when Sky launched its Ocean Rescue campaign nearly two years ago, which raised the possibility that microplastics eaten by seafood and fish would end up in the food chain.
The particles discovered in the samples were between 50 and 500 micrometres wide – and the most common types of plastic involved were polypropylene (PP) and polyethylene terephthalate (PET).
On average, the scientists found 20 particles of microplastic in every 10g of stool.
Lead researcher Dr Philipp Schwabi, from the Medical University of Vienna in Austria, said: “Of particular concern is what this means to us, and especially patients with gastrointestinal diseases.
“While the highest plastic concentrations in animal studies have been found in the gut, the smallest microplastic particles are capable of entering the blood stream, lymphatic system and may even reach the liver.
“Now that we have first evidence for microplastics inside humans, we need further research to understand what this means for human health.”
The research did not determine where each of the plastic particles came from.
A food diary kept by all the participants showed they all consumed food and drink wrapped in plastic. None were vegetarian and six ate sea fish.
Previous studies have found significant amounts of plastic in tuna, lobster and shrimp.
It is estimated that 5% of all plastic produced ends up in the world’s oceans, where it breaks down gradually and gets eaten and absorbed by sea life.
The researchers fear the plastic could also come from the packaging the food is contained in, or the techniques used to process or manufacture it.
Not all experts are worried, with environmental expert Professor Alistair Boxall from the University of York saying: “I’m not at all surprised or particularly worried by these findings. Microplastics have been found in tap water, bottled water, fish and mussel tissue and even in beer.
“We will also be exposed to particles from house dust, food packaging materials and the use of plastic bottles. It’s therefore inevitable that at least some of these things will get into our lungs and digestive systems.”
The results of the study come hours after Environment Secretary Michael Gove launched a consultation on the government’s plan to ban the distribution and sale of plastic straws, drinks stirrers and cotton buds.