The persistent cloaca is one of the most complex and challenging developmental malformations. It is a rare anomaly occurring only in the female newborn and is represented by the association of urogenital sinus with an anorectal malformation (ARM). Each case is probably unique. We report here one such case of cloaca with the VATER association-tracheoesophageal fistula (TOF) with a urogenital sinus, rectovaginal fistula, and an anteposed stenosed anus, along with preaxial syndactyly of the right hand. The spine, renal, and cardiac systems were normal. Interim management was directed towards repair of the TOF and a right transverse defunctioning colostomy. Despite thorough radioendoscopic preoperative investigations, the complexity of the cloacal anomaly was not delineated until surgery. This case is a rather rare combination of an intermediate form of the cloacal-ARM spectrum. Such patients present with many diagnostic and therapeutic problems. Interval surgery should be directed towards decompression of the affected organ systems, and definitive surgery must be carefully planned and, whenever possible, done in a single stage with simultaneous multisystem repair to correct all significant malformations related to the cloacal complex.