Boone made the announcement Wednesday, saying he has known about his heart condition since college but tests done after his routine physical determined he needed surgery. It is not an emergency, but doctors indicated the procedure was needed.
He said doctors told him he could play baseball when he recovers, but he's not sure if he will.
An emotional Boone delivered the news flanked by general manager Ed Wade and manager Cecil Cooper and in front of a somber room filled with teammates and Astros officials.
"It definitely hits home, but I'm doing well with it," Boone said. "I feel like I'm fairly educated on it now. I have a strong faith and a great family and friends and teammates. I really am doing well and I'm ready to tackle this thing and get it behind me and get on with life."
Wade said a local doctor who did the team physicals and team doctor Jim Muntz worked together to conduct tests on Boone because they knew of his condition.
"Unfortunately the test results came out indicating there was an acceleration of the condition that Aaron has been dealing with for a number of years," Wade said.
He has a bicuspid aortic valve, a congenital defect where the valve has only two cusps to manage the flow of blood through the heart, as opposed to the normal three. The surgery has been scheduled for March 26 at Stanford University Medical Center, according to MLB.com.
Cooper rubbed Boone's back as he expressed his concern for the player.
"As a baseball family we're here to support Aaron, as you can see by all the teammates and front office personnel we have here," Cooper said. "And anything he needs we're going to be there to help him out."
Boone said he feels fine, and that he's never had symptoms of the problem.
The third baseman signed with the Astros in the offseason after spending last season with the Washington Nationals. But Boone, 36, isn't sure if he'll ever play for Houston, or any other team, again.
"I think about it a little bit, but at the end of the thought or the end of the day it's about getting this and we'll see where I am a month from now, two months from now, three months from now," he said.
He'll make decisions on his future after he recovers and can research and talk with athletes who have returned to play after heart surgery. He mentioned getting in touch with Golden State's Ronny Turiaf, who had a similar procedure and still plays in the NBA.
If he wants to talk to someone closer, he can look across the clubhouse to reliever Doug Brocail. Brocail did not have open heart surgery, but underwent two angioplasties on his heart in 2006, during which four stents were installed.
"You want the guy here, but there's life after baseball," Brocail said. "[I told him], get this done for you and your kids and if you play baseball again, so be it. If you don't, get it fixed so you can have a normal, healthy life."
Boone has also played for Cincinnati, the New York Yankees, Cleveland and Florida in his 12-year career.