Exercise testing is commonly performed in children for evaluation of cardiac disease. Few data exist, however, on the prevalence, types of arrhythmias, predictors for arrhythmias, and safety of exercise testing in children. A retrospective review of all patients ≤21 years undergoing exercise testing at our center from 2008 to 2012 was performed. Patients with clinically relevant arrhythmias were compared to those not experiencing a significant arrhythmia. 1,037 tests were performed in 916 patients. The mean age was 14 ± 4 years, 537 (55 %) were male, 281 (27 %) had congenital heart disease, 178 (17 %) had a history of a prior arrhythmia, and 17 (2 %) had a pacemaker or ICD. 291 (28 %) patients had a rhythm disturbance during the procedure. Clinically important arrhythmias were noted in 34 (3 %) patients and included: 19 (1.8 %) increasing ectopy with exercise, 5 (0.5 %) VT, 5 (0.5 %) second degree AV block, 3 (0.3 %) SVT, and 2 (0.2 %) AFIB. On multivariate logistic regression, variables associated with the development of clinically relevant arrhythmias included severe left ventricular (LV) dysfunction on echo (OR 1.99, CI 1.20–3.30) and prior history of a documented arrhythmia (OR 2.94, CI 1.25–6.88). There were no adverse events related to testing with no patient requiring cardioversion, defibrillation, or acute anti-arrhythmic therapy. A total of 28 % of children developed a rhythm disturbance during exercise testing and 3 % were clinically important. Severe LV dysfunction and a history of documented arrhythmia were associated with the development of a clinically important arrhythmia.