The 60-year-old former Aston Villa, Derby County and Queens Park Rangers manager, who played six times for England, took over at Crawley last December.
"Crawley Town can confirm that team manager John Gregory is stepping down from his position with immediate effect," the club said in a statement on their website on Saturday.
"John will be undergoing a major open-heart surgery operation at the beginning of January and afterwards will need a lengthy period of recuperation. This operation needs to be done as soon as possible but is not stress related."
Former Wales striker Dean Saunders will take charge of the team on an interim basis.
(Reporting by Ed Osmond, editing by Pritha Sarkar)
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