Gilbert, who rides for the Deceuninck-Quick-Step team, crashed last year on the same descent where Italian rider Fabio Casartelli died during the 1995 Tour. He continued the stage and reached the finish but was later forced him to abandon the race.
The 36-year-old veteran wrote on Twitter: "It's with great disappointment I have to announce that I won't be participating in this year's @LeTour. After my crash and early exit last year I was very motivated to return this year. It would have been my 10th Tour, but unfortunately I will have to postpone those plans."
Gilbert, who won a stage in 2011, won the prestigious Paris-Roubaix one-day classic in April. Alaphilippe, a Frenchman who won the best climber's polka dot jersey last year, will lead Deceuninck-Quick-Step at the Tour, which starts on July 6 in Brussels.
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