Background: Childhood obesity has increased in the last half of the century. The aim of this study was to evaluate the frequency of obesity in the children with congenital or acquired heart disease. Methods: A total of 1410 children were assessed in this study. The study population was composed of 518 children (289 boys, 229 girls) as control group and 892 children (477 boys, 415 girls) as heart disease group. Patients were grouped into four categories: (I) "Clinic control subjects"; (II) "mild heart disease" that has not been treated with either surgical or catheter intervention; (III) congenital heart disease treated with surgical and/or catheter intervention; and (IV) "arrhythmias". A body mass index >= 85th percentile was defined as overweight, >= 95th percentile as obese, and <5th percentile was defined as underweight. Results: We did not detect any association between heart disease and obesity. There was no difference in the rates of overweight, obesity, and underweight between the healthy control subjects and patients with heart disease (8.1%, 13.3%, and 5.0%; 9.0%, 10.7%, and 4.7%, respectively, p = 0.145). All subgroups had a similar prevalence of underweight, overweight, and obesity as the healthy control population. Within the heart disease population, the overall prevalence rates for overweight, obesity, and underweight were similar between the boys and girls. Conclusion: Obesity is a common problem in children with heart disease, at least in general population. It is an important additional risk factor for long-term cardiovascular morbidity and mortality in children with heart disease. Precautions to prevent obesity should be a part of paediatric cardiologist's examination.