We aimed to evaluate the etiologies of constipation in patients with anorectal malformations having a good prognosis for bowel control but a high risk of constipation. We included twenty-five patients from the Odense university hospital in Denmark. Patients were subjected to colon transit time examination and high resolution anorectal manometry (HRAM). The median age was 18 (14–24) and 48% (12/25) were females. Fifty-two % (13/25) of patients were diagnosed with constipation. Types of anorectal malformation were perineal fistula (9/25), rectovestibular fistula (8/25), rectourethral bulbar fistula (5/25) and no fistula (3/25). No difference in neither total colon transit time nor segmental colon transit times were found based on the presence of constipation. Only four of the constipated patients fulfilled criteria for dyssynergic defecation with a dyssynergic pattern at HRAM and prolonged colon transit time. A Type I dyssynergic pattern was dominant in constipated patients (7/13). A Dyssynergic defecation pattern was due to isolated contraction of puborectalis muscle in 9 out of 13constipated patients. We found a dyssynergic pattern during attempted defecation in patients with anorectal malformations disregarded the presence of constipation. In the majority of constipated patients an isolated contraction of the puborectalis muscle was visualized with HRAM.