Polanowicz takes over for JudyAnn Bigby, who announced last month that she was stepping down after six years in the post.
Polanowicz has been the president of St. Elizabeth’s Hospital in Boston for the past two years.
Patrick said he’d tap Polanowicz’ expertise to help implement a new state law aimed at controlling health care costs.
The health and human services secretariat oversees a number of state agencies including the embattled Department of Public Health. That agency has been under increased scrutiny following the arrest of a former state chemist accused of tampering with drug tests, and a deadly meningitis outbreak linked to specialty pharmacy in Framingham that was regulated by the state.