Children undergoing radiofrequency ablation (RFA) are believed to be at increased risk of developing malignancy caused by radiation, although the magnitude of this risk is incompletely understood. We previously reported a strategy to reduce radiation exposure during pediatric RFA. In a cohort of 15 subjects (median age 12 years, range 9 to 17), radiation was measured using dosimeters at 5 sites. The risk of malignancy using measured radiation absorbed dose was calculated. International Council for Radiation Protection 60 risk estimates were applied to calculate absorbed organ doses. Median duration of combined biplane fluoroscopy was 14.4 minutes. Of the 5 dosimeter locations, the right scapular location had the highest median radiation exposure (43 mGy). Incorporating data from the 5 dosimeters, the risk model calculated that the organ with the greatest absorbed dose and at greatest risk of malignancy was the lung, followed by bone marrow, then breast. Thyroid and ovary exposures were negligible. The increased lifetime risk of fatal malignancy was 0.02% per single RFA procedure. In conclusion, with appropriate measures to reduce radiation exposure, the increased risk of malignancy after a single RFA procedure in children is low. These data should be of help counseling families and will contribute to analysis of the relative risk reduction benefits of such novel imaging approaches as a magnetic resonance imaging-based catheterization laboratory.