As most other small inedible objects, a swallowed magnet should eventually pass through the digestive system. Two of them, on the other hand, can interact and create problems as a mother in San Jose discovered.
From the New York Times:
Within 72 hours, Braden complained of mild pain in the left abdomen. He had no other symptoms and was not in any apparent distress, but his parents took him to the emergency room anyway. An X-ray showed what Dr. Sanjeev Dutta, in a case study published on Feb. 4 in The Archives of Pediatrics and Adolescent Medicine, calls “an obvious opacity in the right lower quadrant area of the cecum,” a foreign object near the mouth of the large intestine.
An X-ray five hours later showed that the object was not moving properly. Dr. Dutta’s laparoscopy found the magnets stuck together, pinching bowel tissue.
They were removed when they stuck to the ends of the laparoscopic instrument.