The remnants of caveman genes have been associated with Type 2 diabetes, digestive problem Crohn's disease and lupus and biliary cirrhosis which are liver issues.
It is also associated with thick hair, tough skin and nails and curiously addiction to cigarettes.
Between two and four per cent of the genetic map of Europeans and Asians is believed to be a legacy of interbreeding between Neanderthals and the ancient Homo sapiens.
The two were separate human subspecies who co-existed on Earth for thousands of years until the Neanderthals became extinct around 30,000 years ago.
The study, published in international journal Nature, compared the genomes of 1,004 people with the toe bone of a 50,000-year-old Neanderthal woman.
We may learn more about what Neanderthals themselves were like
Study leader Professor David Reich, from Harvard Medical School, said: "Now that we can estimate the probability that a particular genetic variant arose from Neanderthals, we can begin to understand how that inherited DNA affects us.
"We may also learn more about what Neanderthals themselves were like."
The study found one genetic variant linked to Neanderthals was associated with smoking and was specifically related to Euroepans.
The research also found Neanderthal ancestry could be seen in genes for keratin filaments, a protein that lends toughness to skin, hair and nails.
This may have provided those who migrated out of Africa to the cooler environments of with Eurasia thicker insulation.
Professor Reich added: "It's tempting to think that Neanderthals were already adapted to the non-African environment and provided this genetic benefit to (modern) humans."