The toddler's mother panicked after she noticed that all of the magnets from the family's fridge had gone missing after leaving him for a short period of time.
She rushed her son to a local clinic where doctors performed a scan. They were amazed to see a huge quantity of small, round magnets in his abdomen, the Daily Mail reported.
The boy was then rushed to a hospital near her home in Chelyabinsk, Russia, where surgeons immediately operated him.
"The child had been in the room alone with the magnets and now they were gone. She thought he must have swallowed them," said a clinic spokesman.
Surgeons confirmed her fears when scans found 42 magnets in the child's digestive system.
"Over the years, I had to take a variety of foreign bodies including magnets from young patients," Chief pediatric surgeon Nikolay Rostovtsev, who performed the surgery, said.
"Once I removed about 20 of them, but this incident of our little patient has broken all records," Dr Rostovtsev said.
The boy is now recovering from the abdominal operation at the hospital.
Doctors have appealed to parents to keep a close eye on young children as they play, because they taste new objects as a way to explore their surroundings, the report said.
Parents have been adviced to child proof their homes by doing a careful survey of what their toddler can reach in each room and removing or fixing anything that could be hazardous.
They said children naturally stop putting things in their mouths before they turn four.