(CNN) -- Valentino Rossi revealed he is still fighting pain ahead of the U.S. Grand Prix, as MotoGP championship leader Jorge Lorenzo set the pace in qualifying at Laguna Seca.
World champion Rossi will start on the second row of the grid on Sunday after finishing sixth fastest, in what will be just his second race back after breaking his leg in early June.
Lorenzo, who has a 47-point advantage over Dani Pedrosa in the overall standings, claimed his fifth consecutive pole position -- and the 40th of his career -- as he edged out 2007 world champion Casey Stoner with his penultimate lap of one minute 20.978 seconds.
The Fiat Yamaha rider was the only one to break the 1:21 mark, with Ducati's Stoner clocking 1:21.169.
Andrea Dovizioso headed off Repsol Honda teammate Pedrosa to take third place, while American Ben Spies was fifth in 1:21.679.
Nine-time world champion Rossi clocked 1:21.688 to edge out another U.S. rider, the 2006 overall winner Nicky Hayden.
The Italian revealed that he was troubled more by his shoulder problem than his leg.
"I think it's going to be very difficult tomorrow because this track is a lot harder for me than Sachsenring [in Germany], but I hope I can have a good race," he told the MotoGP website on Saturday.
"There are a few corners where we know we can be a bit faster, so tomorrow morning we will try to make some small changes to the setting to allow that, then I need to get a good start.
"My leg feels better than yesterday, which is good. The problem today is the shoulder because my left one isn't strong enough to compensate completely for the lack of power in my right one, and now I have some pain in both!
"My hope for tomorrow is to be able to finish the race without too much pain and to do the best we can in the circumstances. We didn't go too badly today but we need to improve our setting a little bit to get closer to the leaders.
"Lorenzo and Stoner are very fast but after that there are a few riders quite close together, including me, so it's not too bad."
Dovizioso is third overall on 102 points, 36 behind Pedrosa, with Stoner fourth on 83 ahead of Hayden (78) and Rossi (74) with 10 races to go.