The two-time French Open runner-up, seeded second at this year's tournament, lost to the 114th-ranked Arantxa Rus of the Netherlands 3-6, 7-5, 6-1.
"I started doubting a little bit," said Clijsters, who was playing only her second match since a right ankle injury knocked her out of action. "When you start doubting yourself on any surface, but for me definitely on clay, it's the wrong attitude to have." Two-time French Open finalist Robin Soderling and No. 10 Mardy Fish of the United States also advanced, as did No. 6 Li Na of China and No. 9 Petra Kvitova on the women's side.
Also Thursday, five-time champion Rafael Nadal is scheduled to be back on court _ two days after being stretched to five sets for the first time in his French Open career. Maria Sharapova is also set to play.
Clijsters, who had won her last 15 Grand Slam matches after taking the titles at last year's U.S. Open and this year's Australian Open, failed to convert either match point in the second set.
Playing with her right ankle taped, the Belgian made 65 unforced errors in the match and lost 11 of the final 12 games. Rus finished with only 22 unforced errors and had only eight winners in the entire match.
"My ankle feels fine, so that has absolutely nothing to do with it," Clijsters said. "If I felt like I wasn't ready as much as I would have liked to be, I wouldn't have come here. If I wasn't feeling like I was able to play tough matches, then I wouldn't have made that decision to come here." Clijsters had her first chance to close out the match against the Dutchwoman when leading 5-2 in the second set, but Rus saved the match point and held to make it 5-3 before breaking Clijsters to get back on serve.
"When I was 5-2 down in the second set, I was thinking, 'Just go for it and play more aggressive,"' Rus said.
"And, yeah, that really helped.
"At 6-5 I had a really good serve game, and then I won the set. Then I was thinking, 'Yeah, I can win this match."' Clijsters then had another match point in the 10th game, but Rus saved it again and eventually pushed the score to 5-5.
With the momentum shifting, Clijsters double-faulted for the seventh time _ one of her 28 unforced errors in the set _ to allow Rus to break and serve out the second set.
"She obviously started building up more confidence, started playing a lot better and was really kind of putting me on my back foot all the time. I couldn't really play my aggressive tennis anymore in that third set," Clijsters said.
Clijsters injured her right ankle while dancing at her cousin's wedding in April, sidelining her until the French Open. She last played at Roland Garros in 2006, when she reached the semifinals.
The last time Clijsters was eliminated this early at a major tournament was when she lost in the second round at Wimbledon in 2002.
But since returning to the tour in 2009 following the birth of her daughter, Clijsters has won three of her four Grand Slam titles.
Rus, the 2008 Australian Open junior champion, reached the third round of a Grand Slam tournament for the first time.
Li beat Silvia Soler-Espinosa of Spain 6-4, 7-5, and Kvitova defeated two-time Grand Slam semifinalist Zheng Jie of China 6-4, 6-1.
No. 12 Agnieszka Radwanska of Poland, No. 21 Yanina Wickmayer of Belgium and No. 25 Maria Kirilenko of Russia also advanced to the third round Thursday, while No. 27 Alexandra Dulgheru of Romania lost.
The fifth-seeded Soderling beat Spanish qualifier Albert Ramos 6-3, 6-4, 6-4.
"A win in straight sets is always good," the Swede said.
Also, No. 20 Florian Mayer of Germany lost to Alejandro Falla of Colombia and No. 24 Sam Querrey of the United States lost to Ivan Ljubicic of Croatia.