A cloacal malformation is a congenital malformation in which the urinary tract, gynecological system and distal rectum fail to separate and form a common channel with a single perineal opening. Precise anatomical information is required to plan surgery and predict prognosis for children with this abnormality. Conventional fluoroscopic studies provide limited information, primarily due to the overlap of structures and inability to make accurate measurements. Rotational fluoroscopy and 3-D reconstruction help clarify overlapping structures and allow for precise measurement of the common channel, thereby helping to predict the complexity of the surgical case as well as the long-term prognosis regarding bowel, bladder and sexual function.