The Winnipeg Regional Health Authority says the laptop was taken from the office of a physician working in the Department of Internal Medicine.
It contains information from 322 patients that was gathered over the past 18 months.
Real Cloutier (ray-AL' KLOO'-tyay), chief operating officer for the health authority, says it takes patient privacy seriously.
He says Winnipeg police and the patients affected by the privacy breach have been notified.
Cloutier says the health authority will also conduct its own investigation into how and why this happened.
"We can appreciate how unsettling this must be for patients," Cloutier said in a release Friday.
"We are deeply sorry, and want to assure patients and the public we are looking at every option possible to get the laptop back."