Gilbert had been active towards the tail end of the second week, finishing fourth on stage 13 to Rodez, but has since fallen ill and will not start on Tuesday.
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The Belgian rider has enjoyed a busy but successful 2017 season so far, heading to the Tour de France on the back of victories in the Tour of Flanders and the Amstel Gold Race, before warming up for the Tour with a stage win at the Tour de Suisse.
Quick-Step are yet to announce Gilbert’s race programme for the rest of the season, particularly whether he will race the Vuelta a España ahead of the World Championships in Bergen, Norway in September.
The Tour de France continues on Tuesday with a 165km stage to Romans-sur-Isère where the Belgian team will be hoping to guide Marcel Kittel to his sixth stage win of the race.