Clarke pulled a hamstring while on vacation in the Bahamas just more than a week ago. He pulled out of the Texas Open last week with hopes that rest and treatment would speed his recovery. But on Monday, Clarke said he wasn't fit to play.
Clarke says playing in the Masters is "one of golf's great pleasures." He missed the cut at Augusta National last year.
He plans to continue treatment in the Bahamas and was not sure when he would return to competition.
Clarke was not replaced in the field. There are no alternates at the Masters.
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