The department is responsible for awarding millions each year to research facilities through the Commonwealth Universal Research Enhancement Program (CURE).
"The goal of CURE is critical to health care and an economic driver for our state," said DePasquale. "This is a great way to keep and retain talent, and I want to make sure we are utilizing it to the best of our abilities."
In all, $797 million has supported 1,900 research projects statewide. The annual funding is the result of the 1998 multistate master settlement agreement with the four leading tobacco companies.
Pennsylvania's share of the settlement funds, which has varied from year to year, is the subject of ongoing litigation. An arbitration ruling last year cut almost in half Pennsylvania's roughly $320 million annual payment for 2014. That decision is under appeal.
"Taxpayers can ill-afford to make up this enormous difference," said DePasquale. "The loss of funds will threaten finding cures for deadly diseases, like cancer and heart disease. When you cut funds, you reduce staff and scuttle research that may be the difference between life and death."
The audit initially will include a sampling of CURE grants to five research hospitals across the state, including Children's Hospital of Philadelphia, where researchers have conducted breakthrough research on sickle cell disease and leukemia.
Other institutions, including most of the major health research facilities in Southeastern Pennsylvania, have used the funding to explore new ways to diagnose and treat various cancers and heart disease, as well as smoking cessation and prevention programs.
DePasquale said he hoped to complete the audit by the end of the year.