They took DNA samples from five people and sent them to the companies.
Researchers found that while both companies' DNA scans were accurate, the way they interpreted the results differed greatly, for instance in the criteria used to assess the likelihood that a customer will develop a specific disease.
But researchers warn that even if all companies agreed on the criteria used to interpret results, much remains to be discovered about the factors that play a role in the development of a disease.
Experts believe companies should be better about telling consumers how much is still unknown, and that people should take these tests with a grain of salt.
The findings are published online in the journal Nature.