Nadal recently retook the top spot in the ATP rankings and long ago wrapped up a spot in the yearend World Tour Finals. He is 68-5 on the year with 10 titles and three second-place finishes.
Since winning the U.S. Open a month ago Nadal has played on a Davis Cup match, lost in the finals of the China Open and was beaten in the semifinals at the Shanghai Masters.
"Hi all, sorry to announce that I won't travel to Basel in Switzerland but after very exhausting weeks I have to regroup my fitness and my body," Nadal posted on his Facebook page. "I will do my best to come back to the Swiss Indoors next year."
Nadal has played on the Swiss Indoors twice, losing first-round matches in 2003 and '04.