The finding has surprised many experts, as previous genetic evidence suggested the Neanderthals made little or no contribution to our inheritance.
The result comes from analysis of the Neanderthal genome - the "instruction manual" describing how these ancient humans were put together.
Between 1% and 4% of the Eurasian human genome seems to come from Neanderthals.
But the study confirms living humans overwhelmingly trace their ancestry to a small population of Africans who later spread out across the world.
The most widely-accepted theory of modern human origins - known as Out of Africa - holds that the ancestors of living humans (Homo sapiens) originated in Africa some 200,000 years ago.
While the Neanderthal genetic contribution - found in people from Europe, Asia and Oceania - appears to be small, this figure is higher than previous genetic analysis have suggested.
"They are not totally extinct. In some of us they live on, a little bit," said Professor Svante Paabo, from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.
Professor Chris Stringer, research leader in human origins at London's Natural History Museum, is one of the architects of the Out of Africa theory. He told BBC News: "In some ways [the study] confirms what we already knew, in that the Neanderthals look like a separate line.
"But, of course, the really surprising thing for many of us is the implication that there has been some interbreeding between Neanderthals and modern humans in the past."
... on closer inpection, Bush
sure looks like a Neanderthal...