"You know it happens in the industry, and you see it happen to other players, you don't expected it to happen to you," general manager Jeff Luhnow said.
Cisnero is the latest pitcher to need the surgery, which typically requires a 12-month recovery. Marlins ace Jose Fernandez is expected to need the procedure, and Mets ace Matt Harvey is recovering from his.
Cisnero was called up from Triple-A Oklahoma City on April 25 and appeared in five games with the Astros. He shares the same agent with former Astros pitcher Fernando Rodriguez, who underwent the surgery shortly after he was traded to the A's in February 2012.
Cisnero, 25, made his Major League debut last year and was 2-2 with a 4.12 ERA in 28 games out of the bullpen.
"He's been able to talk to him about the experience and he knows what to expect," Luhnow said of Cisnero's relationship with Fernandez. "He's young and he's got a good arm and I'm sure he'll come back."
Meanwhile, Luhnow said veteran right-handed reliever Matt Albers received a cortisone shot Tuesday in his right shoulder and won't throw a baseball for 10 days while he recovers from tendinitis. He's been on the disabled list since April 22.
The good news for the Astros is an MRI showed some inflammation but no structural damage to Albers' shoulder.
"It's going to be longer than we originally expected, but it's not anything that will hinder him long term," Luhnow said.
With Jesse Crain (biceps tendinitis surgery) having not pitched this year and Albers limited to eight games, two of the three veteran relievers the Astros acquired to improve their bullpen are now on the shelf. Right-hander Chad Qualls remains healthy.
"It's a setback," Luhnow said. "I talked to Crain and he's feeling better every day. We're still unclear as to his return. That's why you try and build up as much depth as you can. Clearly, two-thirds of our master plan to fix the bullpen is not available, and that hurts. We'll overcome it. Fortunately, both of them are expected to return and hopefully they'll come back and contribute. In the meantime, the other guys will step up and it provides opportunity."
Brian McTaggart is a reporter for MLB.com and writes an MLBlog, Tag's Lines. Follow @brianmctaggart on Twitter. This story was not subject to the approval of Major League Baseball or its clubs.