Deaths have been reported following radiofrequency catheter ablation (RFCA), but the mortality rate in children has not been defined. This study sought to analyze the incidence and the factors associated with mortality related to RFCA. Ten of 4,651 cases (0.22%) reported to the Pediatric RFCA Registry resulting in death were reviewed and compared with a matched control group (n = 18). Death occurred in 5 of 4,092 children (0.12%, ages 0.1 to13.3 years) with structurally normal hearts. Death was related to traumatic injury, myocardial perforation and hemopericardium, coronary or cerebral thromboembolism, and ventricular arrhythmia. All cases were left-sided (p = 0.019 vs right or septal) supraventricular arrhythmias with radiofrequency applications in the systemic atrium and/or ventricle, and all procedures were successful. Mortality occurred in 5 of 559 children (0.89%, p = 0.001 vs normals, ages 1.5 to 17.4 years) with structural heart disease. No new pathology except the mural radiofrequency lesions was seen at autopsy. Those with structurally normal hearts who died were smaller (32.7 vs 55.6 kg, p = 0.023) and had more radiofrequency applications (26.3 vs 8.7, p = 0.019) than those who survived. No differences were demonstrated for those with abnormal hearts. Operator experience was not different (deaths 103 ± 106 vs controls 117 ± 125, p = 0.41). Mortality associated with pediatric RFCA is rare, but is more frequent when there is underlying heart disease, lower patient weight, greater number of radiofrequency energy applications, and left-sided procedures. Operator experience does not appear to be a factor leading to mortality.