Second seed Kim Clijsters retired from her fourth round match in the middle of the second set on Tuesday, handing victory to France's Marion Bartoli.
Clijsters won the first set 6-3 but then called for the trainer early in the second set before packing it in 24 minutes in with Bartoli leading 3-1.
Clijsters complained of having right shoulder problems this week and has been getting regular treatments for the injury, but it all caught up to her against Bartoli.
"I just felt on every serve or forehand that came in a little high that something was not right, that something was not suppose to be there," Clijsters said.
"I still felt I could have won. I could have taken pain killers but I don't want to risk tearing it and I don't want to be in a situation where I am taking medication to cover something up.
"It makes me realize I am not the youngest out there and maybe I don't recover as fast."
Clijsters said she started to have problems with the arm during the Aussie Open in January. She said she couldn't remember the last time she pulled out in the middle of a match.
"A lot of times it is important to rest and listen to your body even though it goes against what other people might be saying," she said.
The injury dashes any hope Clijsters had of regaining the world number one ranking at this event. Clijsters needed to post a better finish than Dane Caroline Wozniacki to do that.
Clijsters, who won Indian Wells in 2005 and 2003, ended her streak of reaching the final in her last five tournaments.
Clijsters will now head to Florida to try and get ready for the Miami tournament.
"I need a few days rest and to have some tests done," Clijsters said.
Bartoli advanced to the quarterfinals where she will face former world No. 1 Ana Ivanovic who beat defending champ Jelena Jankovic 6-4, 6-2 in an all-Serbian matchup earlier on Tuesday.