Constipation, incontinence and gastrointestinal symptoms are common in children operated for anal atresia, but the frequency of recurrent abdominal pain (RAP) and the relation to bowel problems has to our knowledge not been described in the literature. From the medical records a total of 40 children in the age of 9-13 years old operated for AA were asked to fill out a questionnaire, and a reply was received form 39. The questionnaire had 52 questions, the majority of the questions were yes/no and a few were interval questions. The questionnaire was divided into three sections: 1) abdominal pain, 2) dyspepsia and 3) constipation. This was compared with the results of a similar questionnaire among 1142 schoolchildren in the age of 9-13 years randomly selected from Odense County, Denmark. A total of 15 out of 39 patients (38%) operated for AA fulfilled the criteria of RAP compared to 12% in the background population (P < 0.0001). Ten (66%) of the AA-children with RAP fulfilled the Rome II criteria of constipation, and four (17%) of the AA-children without RAP (P < 0.003). In the background population 12% of the children with RAP fulfilled the constipation criteria, and 2% of the children without RAP (p < 0.0001). There was no significant difference in the frequency of RAP in children with high and low AA. In conclusion, the frequency of RAP was significant higher in children operated for anal atresia compared to the background population, and in both groups there was s significant correlation between RAP and constipation. The correlation between constipation and RAP in children operated for AA might reflect insufficient bowel management in these children. Improved physiological tests and questionnaires are needed to identify the characteristics of bowel function in children operated for AA to give a specific treatment, which might decrease the prevalence of RAP and improve the quality of life in these children.