Researchers say the need for the tests probably outweigh a slightly higher brain cancer risk later in life for children who get several CT scans.
The use of CT scans has risen rapidly since they were introduced 30 years ago.
International researchers studied nearly 180,000 patients under age 22. The scientists looked at data measuring radiation doses from the scans.
The children who later developed leukemia or brain tumors were compared to a group of people who got a very low dose of radiation to the same parts of their bodies.
Researchers concluded the risk of brain tumors was tripled if children had two to three scans and the risk of leukemia was tripled with five to 10 scans. But they emphasized these were rare diseases and that the higher risk was still small.
The research is in the journal, Lancet.