Endomyocardial biopsy in children remains important in the evaluation of cardiomyopathy, myocarditis, and rejection following cardiac transplantation. We sought to evaluate the morbidity associated with endomyocardial biopsy on the basis of a large experience from a single institution. We reviewed records of all endomyocardial biopsies performed at our institution. Complications were defined as adverse events resulting from the biopsy requiring intervention or additional observation. We also reviewed the most recent echocardiogram from all the patients for the presence and severity of tricuspid valvar regurgitation. Between November 1986 and April 2002, we performed 1051 endomyocardial biopsies in 135 patients ranging in age from 9 days to 18 years. The internal jugular vein was the site of vascular access in 68% of the procedures. There were 10 acute procedural complications requiring intervention or additional observation. Severe tricuspid regurgitation developed in two patients who had undergone multiple biopsies after cardiac transplantation, one of whom underwent subsequent replacement of the tricuspid valve. There were no deaths or cardiac perforations. The total incidence of morbidity was 1.1%. No demographic or procedural factors were identified to be predictive of complications. In experienced hands, therefore, endomyocardial biopsy can be safely performed in children with very low morbidity.