The researchers at Oxford University and Plymouth University compared genetic data from fossils of Neanderthals and another group of ancient human ancestors called Denisovans to data from modern-day cancer patients.
They found evidence of Neanderthal and Denisovan viruses in the modern human DNA, suggesting that the viruses originated in our common ancestors more than half a million years ago.
This latest finding, reported in journal Current Biology, will enable scientists to further investigate possible links between ancient viruses and modern diseases including HIV and cancer.
Around 8 per cent of human DNA is made up of 'endogenous retroviruses' (ERVs), DNA sequences from viruses which pass from generation to generation. This is part of the 90 per cent of our DNA with no known function, called 'junk' DNA.
"I wouldn't write it off as "junk" just because we don't know what it does yet," said Dr Gkikas Magiorkinis, an MRC Fellow at Oxford University's Department of Zoology.
"Under certain circumstances, two "junk" viruses can combine to cause disease - we've seen this many times in animals already. ERVs have been shown to cause cancer when activated by bacteria in mice with weakened immune systems," said Magiorkinis.
Gkikas and colleagues are now looking to further investigate these ancient viruses, belonging to the HML2 family of viruses, for possible links with cancer and HIV.
"How HIV patients respond to HML2 is related to how fast a patient will progress to AIDS, so there is clearly a connection there," said Magiorkinis, study author.
"HIV patients are also at much higher risk of developing cancer, for reasons that are poorly-understood. It is possible that some of the risk factors are genetic, and may be shared with HML2. They also become reactivated in cancer and HIV infection, so might prove useful as a therapy target in the future," Magiorkinis said.
The team are now investigating whether these ancient viruses affect a person's risk of developing diseases such as cancer.
Combining evolutionary theory and population genetics with cutting-edge genetic sequencing technology, they will test if these viruses are still active or cause disease in modern humans.