Vaccine Safety Study Act - Requires the Secretary of Health and Human Services (HHS), acting through the Director of the National Institutes of Health (NIH), to conduct a comprehensive study to: (1) compare total health outcomes, including the incidence and risk of autism, between vaccinated and unvaccinated U.S. populations; and (2) determine whether exposure to vaccines or vaccine components is associated with autism spectrum disorders, chronic conditions, or other neurological conditions.

Requires the Secretary to seek to include in the study U.S. populations that have traditionally remained unvaccinated for religious or other reasons.

Directs the Secretary to ensure the preservation of all data, including all data sets, collected or used for purposes of the study to facilitate further research by the Secretary or others.

Declares that nothing in this Act shall be construed to authorize the conduct or support of any study in which an individual or population is encouraged or incentivized to remain unvaccinated.