In 2006, he was in advanced negotiations with Yamaha, but after they dropped him he settled on an alliance once more with team manager Lucio Cecchinello on a Honda RC211V, on a one-bike team new to the series for the 2006 Season, Team LCR. He secured a ride with the factory Ducati team for the 2007 season, joining Loris Capirossi on the new 800cc Ducati Desmosedici GP7. 6 poles and 10 race wins took him to his first GP title, by a margin of 125 points over Dani Pedrosa, which he built during the second half of the season. He opened the 2008 season with a victory at Qatar, before a run of two races without a podium. He remained with Ducati for the 2009 season with new team mate Nicky Hayden, with a further option for a 4th season in 2010. He qualified on pole for the season opener in Qatar, and was leading the race when he crashed out. In 2011 he joined Honda Racing Corporation after four years at Ducati Corse.