Lyon, who started the season as Houston's closer, missed more than a month on the DL with the same problem before he was activated last Thursday. He has struggled in his three appearances since, allowing a home run in each and a total of eight earned runs.
Astros manager Brad Mills said Lyon's arm has been bothering him and that they decided to place him on the DL after consulting with doctors on Wednesday.
"We had a chance to sit down with Brandon this afternoon (and) he admitted he still had discomfort in his biceps tendon," Houston general manager Ed Wade said. "It doesn't make any sense for him to go out and be heroic with the way he's feeling now."
He's scheduled to see Dr. Lewis Yocum in Los Angeles on Friday for a second opinion. Lyon said the situation is scary and that he believes surgery could be an option.
"If you're feeling any pain that you don't think you should be feeling, you want to know what's going on," he said. "I don't know what to think at this point."
Wade said he thinks Lyon may have downplayed his discomfort because he wanted to play.
"This is a little bit of a case of Brandon wanting to help the club and wanting to get back to the point where he was a year ago," Wade said. "He has just been physically unable to perform at the level that he's been capable of in the past."
Lyon had said his arm felt good after each of his outings since coming off the disabled list, but Mills said sometimes players with tendinitis feel fine once they get warmed up, only to have the pain return.
"Once your arm gets loose and gets warm, you start feeling like you're OK. Even though it's not OK, it starts feeling OK," Mills said. "Once he gets warmed up and gets throwing he feels like he's OK, even though he's not able to have the stuff he's had before."
Lyon said he had trouble figuring out if he needed to shut it down again or not.
"It's hard to decide if you're a little banged up or really hurt," he said. "When I go out there, I've pitch through some things before, so it's hard for me to decide whether I can throw through it or not. Right now, it's just time to explore other options and see something different, so I can get this squared away so I can feel like I'm helping the team."
Lyon is 3-3 with an 11.48 ERA in 15 games this season. Last year, he had 20 saves with a 3.12 ERA in 79 appearances.
Left-hander Fernando Abad was recalled from Triple-A Oklahoma City to take Lyon's spot on the roster.