The third seed was due to play to play a third-round match against Poland's Agnieszka Radwanska.
"I'm really disappointed to have to withdraw from Eastbourne this morning," the Czech player said.
"I felt my hamstring in the Birmingham final and although I played with tape in my match here yesterday, when I woke up this morning it felt worse.
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"With Wimbledon around the corner I couldn't take the risk of making it worse by playing today."
Kvitova won the Wimbledon title in 2011 and 2014.
(Reporting by Martyn Herman; Editing by Keith Weir)
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