It comes two years after he had 13 inches of his colon removed because of an inflammation and narrowing of the large intestine.
The Vatican said Francis, 86, would be put under general anesthesia and would be hospitalised for several days.
The pope was undergoing what the Vatican said was a "laparotomy and abdominal wall plastic surgery with prosthesis" to treat a "recurrent, painful and worsening" constriction of the intestine.
A laparotomy is open abdominal surgery. It can help a surgeon both diagnose and treat issues.
"The stay at the health facility will last several days to allow for the normal post-operative course and full functional recovery," the statement said.
In July 2021, Francis spent 10 days at Gemelli to remove a section of his large intestine. He had suffered what the Vatican said was a severe inflammation and narrowing of the colon.
In an interview with The Associated Press in January, Francis said the diverticulosis, or bulges in his intestinal wall, that prompted the 2021 surgery, had returned.
Francis went to the Gemelli on Tuesday for what the Vatican said were medical tests. It revealed no details at the time.
Francis, 86, had appeared in good form on Wednesday morning at his audience in St Peter's Square.
The Argentine pope had part of one lung removed when he was a young man. He also suffers from sciatica nerve pain and has been using a wheelchair and walker for more than a year because of strained ligaments in his knee.