The 32-year-old underwent medical tests on Thursday morning that revealed a cyst in the buttock region as well as severe sores which means he will not return to competitive action until 2014.
"It needs time to heal as it's one of the most sensitive injuries for a cyclist," explained the Belgian star who won the 2005 world championship road race in Madrid.
"I am very disappointed because I feel good physically.
"After my stage win on the Tour of Wallonie (end of July), I had high hopes for the rest of the season," he continued.
"In 2011, I had exactly the same injury and when I came back, I had one of my best seasons in 2012," he added in reference to big wins that season including his third Tour of Flanders, fourth Paris-Roubaix as well as a third win at the Gand-Wevelgem.
He has also won six stages on the Tour de France and won the green jersey as points winner in 2007.
The world championships will be held in Florence, Italy from September 22 to 29.