Overweight and obesity rates have risen dramatically in the United States, with subsequent detrimental comorbidity risks. The rates for obesity among children with congenital and acquired heart disease have rarely been reported. A retrospective cross-sectional study was conducted to determine the prevalence of overweight and obesity in children with heart disease and to identify subgroups at increased risk. A total of 795 cases were identified from a chart review of patients presenting to an urban center’s Pediatric Cardiology Program between 1 January and 31 December 2006. A body mass index (BMI) at the 85th percentile or higher was defined as overweight, and a BMI at the 95th percentile or higher was defined as obese. Subjects with comorbidities affecting body habitus were excluded from the study. Overall, overweight and obesity rates were similar to national data. No significant differences in overweight or obesity rates were detected between heart disease and non-heart disease groups (P = 0.50). According to multivariate analysis, Hispanic ethnicity and male gender were the only predictors of obesity. This study shows that children with heart disease are not immune to the common predictors of obesity such as gender and ethnicity and that the future care of children with heart disease should include general discussions about the risks for obesity.