Purpose: This study aimed to assess the results of endomyocardial biopsy from the right ventricle to establish the possible cause for drug-refractory arrhythmias in children. Materials and methods: We enrolled 19 consecutive young patients with drug-refractory arrhythmia, from 2010 to 2013, who underwent endomyocardial biopsy. Inclusion criteria were as follows: age < 18 years with a structurally normal heart or mild changes in a structure of the heart initially diagnosed as arrhythmia-induced cardiomyopathy. Overall, 86 biopsies were performed in 19 patients. Histopathological analysis, immunohistochemistry, and polymerase chain reaction were used for the interpretation of the endomyocardial biopsy. Results: The mean age of the patient population was 14.1 +/- 2.9 year (range from 7 to 17 years). All these patients had a history of drug-refractory arrhythmia for > 5 months (mean 30 months). Patients underwent a complete history investigation, physical examination, laboratory studies, echocardiography, electrocardiography, treadmill test, and Holter monitoring before endomyocardial biopsy; two patients with arrhythmogenic right ventricular dysplasia had implantable cardioverter defibrillator implantation and further appropriate successful device shocks. Myocarditis was diagnosed based on histopathological and immunohistological analyses in nine (47.4%) patients. Polymerase chain reaction was positive for viral genome in four of them; five patients had active myocarditis. Radiofrequency ablation was performed in 17 patients; five out of six (83%) endomyocardial biopsy-proved myocarditis patients had successful radiofrequency ablation. No significant complication was reported during ablation and endomyocardial biopsy. Conclusions: Approximately half of the children with drug-refractory arrhythmia had unsuspected myocarditis according to the results of the endomyocardial biopsy.