The Russian will face seventh seed Marat Safin, who beat Julien Benneteau of France 6-4 6-0 6-2.
There were no such problems for top seed Marat Safin, who beat Brazilian Fernando Meligeni 6-4 7-6.
Meanwhile Marat Safin went through to the quarter-finals when Fabrice Santoro was forced to retire in the third set.
One of tennis' brightest young stars, Marat Safin has it all - talent, power, flair, and a slightly suspect temperament.
Russia have named Marat Safin in their squad, despite his wrist injury, along with Yevgeny Kafelnikov, Mikhail Youzhny and Nikolay Davydenko.
Earlier, Marat Safin bade farewell to professional tennis with a 6-4 5-7 6-4 defeat by U.S. Open champion Juan Martin Del Potro.
Roddick lost to Janko Tipsarevic, while Djokovic went out to Marat Safin.
The grass-based tournament will feature world number three Andy Murray and three former world number ones: Andy Roddick, Lleyton Hewitt and Marat Safin.
Although still only 21, Federer is firmly established in the top 10 alongside other youngsters Lleyton Hewitt, Marat Safin and Juan Carlos Ferrero.
Meanwhile Russian Nikolay Davydenko defeated Jose Acasuso from Argentina 6-4 6-3 while the fourth-seeded Russian Marat Safin beat Jarkko Nieminen from Finland 6-3 6-3.
And Wimbledon champion Goran Ivanisevic is joined in the draw by Frenchman Sebastien Grosjean, who finished 2001 as world number six, and Australian Open finalist Marat Safin.
Last year, Federer struggled past Sweden's Robin Soderling in his first match, losing the first set, but went on to beat Russia's Marat Safin in the final.
Ferrero's time at Roland Garros looked to have come this year when he beat Andre Agassi and Marat Safin on the way to his first Grand Slam final.
Third seed Lleyton Hewitt was beaten 7-6 (7-1) 6-4 by Frenchman Arnaud Clement, who now meets Marat Safin after the Russian beat Wesley Moodie 7-6 (7-5) 7-6 (11-9).
Meanwhile, in the men's section, local favorite Marat Safin opened his final Kremlin Cup campaign by ousting defending champion and Shanghai Masters winner Nikolay Davydenko in the first round.
Czech Tomas Berdych , meanwhile, ended the Asian portion of Marat Safin's career, with the Russian set to retire in a month, as he came through 3-6 6-4 6-4.
The run began at the 2000 US Open where he was thrashed in the final by a 20-year-old Marat Safin, a match seen by many as symbolic of the end of an era.
Another final in the Masters Series at Indian Wells, before destroying Gustavo Kuerten and Marat Safin on his way to the Masters title in Rome finished off an excellent start to the year.
Marat Safin earlier beat Juan Ignacio Chela 6-7 7-5 7-5 6-1 in the first match of the day, and Russia now just need to win Saturday's doubles to secure a place in the final.
The top seed - still yet to drop a set in the tournament - will face Marat Safin or Feliciano Lopez in Friday's semi-final, and neither will hold much fear after a supreme display against Ancic.
Croatia's Cilic beat Spain's 13th seed Fernando Verdasco 6-2 6-3 in his second-round match and the 19-year-old will undoubtedly prove to be a tougher opponent than Bolelli, who was a late replacement for Marat Safin in the competition.
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