Abstract Purpose Megarectosigmoid (MRS) is commonly seen in children with anorectal malformations (ARM) and contributes to the high incidence of constipation. Surgical resection has been advocated by some, whereas others propose intense bowel management as the treatment of choice. The aim of this study was to evaluate outcome of both bowel function and configuration after surgical or conservative treatment of MRS in ARM patients. Materials and methods The study included 79 patients with ARM, excluding perineal fistula, (48 boys, 31 girls) from 1986 to 2007. MRS was diagnosed at colostomy formation or contrast enema performed in the neonatal period. Early in the period, the majority of the patients were treated surgically, whereas in the late 1990s, a conservative approach with intensified bowel treatment was implemented. Contrast enema and bowel function investigations were performed repeatedly during follow-up. Results MRS, according to radiological criteria, was diagnosed in 26/97 (33%) of the ARM children. Bowel functional outcome was similar regardless of surgical or conservative treatment and comparable to function in ARM children with non-MRS. The radiological signs of rectal dilatation and elongation disappeared after surgical intervention, but normalisation of the rectosigmoidal configuration was also seen with age in the conservative group. Conclusions Bowel functional outcome in ARM children with MRS was similar after either surgical or conservative treatment during follow-up .The radiological signs of rectal dilatation and elongation disappeared also in the conservatively treated patients over time.