Letang, 26, began feeling dizzy last week and tests later confirmed the stroke.
He has had a small hole in the wall of his heart since birth but specialists say the condition is not career threatening and can be treated with blood thinners.
His defect, which occurs in all individuals before birth but usually seals shut, could have led to his stroke, the Penguins said in a news release.
"Kris had one brief episode of dizziness and nausea last week," Penguins general manager Ray Shero said in a statement.
"We held him out of the Los Angeles game Thursday night, and when he continued to feel ill, tests conducted in Phoenix on Saturday gave us the first indication of his condition.
"Further testing then was conducted when he returned to Pittsburgh, and he continued to undergo a battery of tests here this week."
Letang will be re-evaluated after six weeks of treatment by University of Pittsburgh Medical Center doctors.
Letang, who was selected 62nd overall by the Penguins in the 2005 NHL Entry Draft, has been cleared to go on vacation with his family during the NHL's Olympic break.
"It obviously was a shock to get the news but I'm optimistic that I can overcome this and get back on the ice," Letang said.
"I hope that by making my condition public at this time, I can help other people by encouraging them to seek medical help if they experience some of the symptoms associated with a stroke - regardless of their age or general health."
Letang, a finalist for the Norris Trophy as the NHL's top defenseman last season, has 10 goals and 18 points in 34 games this season.
- Ice Hockey