The youngster, who has not been named, fell into a critical condition last year when the magnets attracted to each other and clamped around his appendix causing it to burst. Remarkably - it's believed he swallowed the magnets four months earlier, when his older sister brought them home from a school trip.
The case which has now been documented in the 'Ulster Medical Journal' is the first ever of its kind to cause a burst appendix.
In October 2007 the little boy was admitted to Altnagelvin suffering from tummy pain, cramps and a high temperature. Radiologists who x-rayed him then discovered a foreign body in his tummy area.
The next day the little boy woke in severe pain when he began suffering from peritonitis, an inflammation of the abdominal walls which can be caused by a burst appendix.
This condition can be fatal if not treated immediately.
Quick thinking doctors then performed a laparotomy, a surgical incision into the abdomen, and discovered a tear to the boy's appendix.
They also found and removed several magnets which had become attracted to each other on either side of the appendix, causing it to burst when it became trapped tightly between them.
School trip
His mother remembered the magnets had been brought home from a school trip three to four months previously.
The three year-old has since made a full recovery - however the details have only been revealed in an article in the current edition of the 'Ulster Medical Journal', published by the Ulster Medical Society.
It was written by Andrew L Robinson, Janne Bingham and Ronald LE Thompson, who were all involved in the boy's care at Altnagelvin Hospital.
Professor Patrick J Morrison of Belfast City Hospital, who is honorary editor of the 'Ulster Medical Journal', said the little boy could have died had the problem not been spotted and treated.