Clijsters, the current US Open and Australian Open champion, issued a statement through the referees office saying she had injured her foot at the Den Bosch Open on Tuesday.
"I'm very, very disappointed to have to withdraw from Wimbledon after injuring my foot again at the tournament in Hertogenbosch," said Clijsters, who was the second seed.
"At this moment I feel frustrated that it has to happen now before one of my favourite tournaments.
"I've always enjoyed being a part of the Wimbledon atmosphere but I have no other choice now but to rest, recover and to not play tennis for a few weeks."
The Belgian's withdrawal means last year's runner-up Vera Zvonareva from Russia becomes the second seed having originally been seeded three.
The popular Clijsters, who won the 2009 US Open just three tournaments into a comeback from a two-year retirement in which she gave birth to a daughter, has had her season disrupted by injury since beating China's Li Na to win the Australian Open.
She injured her ankle while dancing at her cousin's wedding, resulting in a two-month lay-off, and although she returned to play in the French Open she struggled and was knocked out in the second round by Dutch world number 114 Arantxa Rus.
Serena Williams, the reigning Wimbledon champion who has just returned from an 11-month absence because of injury and health problems, rises to number seven seed.
The seeding committee had earlier bumped up the American from her world ranking of 26 to take into acccount her formidable record at the All England Club.
With Clijsters out, Williams' chances of a stunning comeback to claim a fifth Wimbledon singles title will be enhanced as will the prospects of sister Venus, who is 23rd seed, after her return from a five-month injury break in Eastbourne this week.
Last year's beaten Wimbledon semifinalist, Tsvetana Pironkova of Bulgaria, is seeded 32, meaning she will avoid any of the big names until the third round.
Querrey pulls out
American Sam Querrey has withdrawn from an arm injury. The big-serving Californian complained of arm pain at Queen's Club last week where he was surprisingly beaten by British wildcard James Ward.
Querrey, ranked 40 in the world, won the Queen's tournament last year and went on to reach the fourth round at Wimbledon where he lost to Britain's Andy Murray.
The American number three's place in the draw will go to a lucky loser from the qualifying tournament.
