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OBJECTIVE Until recently, surgeons have been posed with a dilemma—whether or not they should preserve the terminal end of the distal rectal pouch and the fistula region in anorectal malformations (ARMs). A detailed histological study of this region was conducted to establish a consensus for preserving or excising this region for reconstruction of ARMs. METHODS Histopathological examination using haematoxylin and eosin-stained sections of the terminal portion of the distal rectal pouch and proximal portion of the rectourogenital or rectoperineal connection was performed in 60 cases of high, intermediate and low ARMs. RESULTS Distorted internal sphincter was present in 93.3% of high, 90% of intermediate and 100% of low ARMs. The proximal fistula region was lined by transitional epithelium in 50% of cases, and anal glands were present in 83.3% and anal crypts in 68.3% of cases. The rectal pouch in the region of the internal sphincter and fistula was aganglionic in all cases. CONCLUSION This study shows that the terminal end of the distal rectal pouch and proximal fistula region possess distorted anal features with aganglionosis, and contradicts the recommendation that this region should be reconstructed in patients with malformations.