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Purpose. Congenital heart disease (CHD) is reported to be associated with Hirschsprung disease (HD). The aim was to evaluate any differences between children with HD with and without CHD, respectively, with regard to patient characteristics, medical care, and patient reported bowel function. Method. This is a retrospective chart study and a cross-sectional long-term follow-up of patients older than 4 years old, including all children with HD operated on with transanal endorectal pull-through (TERPT) at a tertiary center of pediatric surgery. Information about patient characteristics, diagnostics, surgery, and medical care was compiled. At long-term follow-up, bowel function was assessed by Bowel Function Score. Results. Included were 53 HD-patients, 13 with CHD and 40 without CHD. Children with CHD more commonly presented with failure to thrive; 4 (23%) compared to those without CHD (0%) (p<0.01). In the long-term follow-up, including 32 patients (6 with CHD), constipation was more commonly reported by children with CHD 5 (83%) than by children without CHD 4 (27%) (p=0.01). No differences were shown in the other parameters such as fecal control and incontinence. Conclusion. HD-patients with CHD more commonly presented with failure to thrive and more frequently reported constipation than HD-patients without CHD. The findings indicate that HD-patients with CHD might need special consideration in their initial care and long-term follow-up.