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Abstract Complete hind gut and anal canal duplication is a rare entity, usually remaining asymptomatic till the disease comes to light due to associated anomalies or due to cosmetic reasons. Classical imaging consisting of barium enema examination served a limited role, in terms of depicting the length of gut segment involved. Technical advances in magnetic resonance imaging (MRI) with three-dimensional (3D) reformations cannot only solve the above purpose but further evaluate key points needed for surgical planning. The present technical report lays out a systematic module for evaluation of various aspects of complete hindgut duplication, critical for management. The role of 3D MRI is emphasized upon, for evaluation of pelvic floor and anorectum, even in infants with a distorted anatomy.