Boonen is slated to head back to Belgium on Sunday to have medical examinations to determine the source of the pain.
"The entire day was OK, a little bit painful but OK," Boonen said. "I worked for the team without particular problems. Then in the final, at about 30 km from the finish, I did a wrong movement to avoid a pothole in the road, and suddenly I got really bad pain on the right side of my chest. I couldn't breathe. That's why I decided to stop. It's a pity — my condition is good and here the team is fantastic, there is a great atmosphere. It's hard to leave the team here, but I have to do what is best for my health leading up to the Olympics."
Boonen chose his season schedule specifically with the Olympic Games and world championships in mind, skipping all three Grand Tours in favour of these races.
Earlier this season he won stages in the Tour de San Luis and Paris-Nice as well as the overall Tour of Qatar before going on a romp in the Classics where he claimed the E3 Prijs, Gent-Wevelgem, Tour of Flanders and Paris-Roubaix.
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