The 79-year-old Swiss official, FIFA president for 17 years and only reelected on Friday, said a special congress would be called as soon as possible to elect a successor.
Blatter said that the scandal-tainted FIFA needs "profound reconstruction" and that he had "thoroughly reconsidered" his presidency since his reelection.
He added that the vote "does not seem to be supported by everybody in the world of football."
His resignation came less than a week after Swiss police arrested seven FIFA officials, including two vice presidents, at a Zurich hotel.
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