In a Red Bull Indianapolis Grand Prix qualifying session that was marred with heavy crashes, it was Pedrosa who grabbed pole position in front of Jorge Lorenzo and Andrea Dovizioso.
Pedrosa's teammate Casey Stoner remains a doubt for Sunday's race, while Ducati Team's Nicky Hayden has been ruled out after suffering concussion.
Pedrosa put in a new fastest ever lap in the high 1.38s, relegating Yamaha Factory Racing's Jorge Lorenzo into second on the grid, after he had struggled with his bike in the preceding sessions. Monster Yamaha Tech 3's Andrea Dovizioso completes the front row, having improved steadily all weekend on his satellite machine.
Heading up the second row in fourth is Lorenzo's teammate Ben Spies, who did incredibly well to walk away from a big crash whilst pushing hard on a hot lap. LCR Honda MotoGP's Stefan Bradl will be very pleased with his day's work, after the German rookie managed to put his bike fifth on the grid.
Repsol Honda's Casey Stoner, who set the sixth-fastest time, suffered a monstrous highside early in the session, causing the red flag to appear, which resulted in small marginal fractures in the ankle. He is undergoing further checks at the Indianapolis Methodist Hospital to confirm his injury and determine his race fitness for Sunday.
Ducati Team's Nicky Hayden was viciously thrown off his bike in the same bend as Stoner and Spies (Turn 13), in the latter part of the session, briefly rendering him unconscious. The red flag was once again shown while Hayden received medical attention. He was spared any serious injuries, though has been declared unfit to race and fractures to his metacarpus. His time would have placed him eighth on the grid.
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This moved San Carlo Honda Gresini's Álvaro Bautista into eighth, with Power Electronics Aspar's Randy de Puniet putting in a terrific performance to place ninth on his CRT machine.
Ducati's Valentino Rossi could only manage 10th place, after suffering a scare in turn 13 with his bike, causing him to abort his fast lap. Attack Performance's Steve Rapp and GPTech's Aaron Yates, both CRT wildcards this weekend, managed to qualify for the race, in 22nd and 23rd place respectively. Many of the riders spoke out about the track surface after the qualifying session citing safety concerns after the three heavy crashes.
Pramac Racing Team's Héctor Barberá, who has been replaced by Toni Elías after fracturing three vertebrae in his back, is currently on his way back to Barcelona for further medical assessments.
Under sunny skies at the Red Bull Indianapolis Grand Prix it was Pons 40 HP Tuenti's Pol Espargaró who stormed to pole position in front of Marc Márquez and Andrea Iannone in Moto2TM qualifying.
And it was Red Bull KTM Ajo's Sandro Cortese who was on top from during an eventful qualifying for the Red Bull Indianapolis Grand Prix as he took a superb pole position ahead of Danny Kent and Maverick Viñales in Moto3.