Abstract Objective  There are no in vitro studies of congenital pouch colon (CPC) associated with anorectal malformation (ARM) to understand its mechanism of contractility. There is no consensus regarding the utilization of the CPC in repair of anorectal malformation. In view of the above, it was decided to carry out detailed in vitro physiological study of the excised CPC. Method  The excised specimens of CPC were taken and 15‐ to 20‐mm long both longitudinal and transverse strips of muscle were obtained both from the proximal and distal part. Contraction was recorded using software chart‐5 for windows. Drugs used were acetylcholine, histamine, adrenaline, atropine and pheniramine maleate. The amplitude of contractions was converted to tension gram and then the tension so developed was expressed as tension per unit mass (per gram of wet tissue). Results  There were total of 21 specimens of high ARM with CPC. Five specimens were of the complete pouch, which did not show a response to any drug and the remaining 16 had an incomplete pouch. The mean longitudinal and circular muscle contractions of these 16 samples were statistically higher for the proximal segment than the distal segment both for acetylcholine and histamine. The effect of atropine was not significant but that of adrenaline and pheniramine maleate were significant on the distal segment muscle. Conclusion  Congenital pouch colon being deficient or having poorly developed receptors in their wall can not function properly as a reservoir for faeces and, hence, it should be excised to allow adequate function.