On 27 April, Boonen tested positive for cocaine for the third time (the first, in November 2007, had not previously been made public). He was suspended by his team, , on 9 May. He began racing again in the Critérium du Dauphiné Libéré. In June, he won the national championship. After initiating legal proceedings he was allowed to compete in the Tour de France, just one day before the start on 3 July 2009. He pulled out, due to illness on 18 July, before the 15th stage.