Congenital anorectal malformations are found in many forms, and are frequently associated with other anomalies, especially of the spinal cord, spine, and urogenital system. Decisions concerning initial management of children with anorectal malformations can be made only after accurate determination of (a) the level and type of malformation, (b) the type of fistula, (c) the developmental state of the sphincter muscle complex, and (d) the presence of associated anomalies. Magnetic resonance imaging has proven to be the only modality to answer all these crucial questions, and has contributed to a better insight in the morphology and pathogenesis of such complex congenital malformations.