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PURPOSE To study the detailed anatomy of cloacal anomalies using the multiplanar capabilities of MRI in addition to other available modalities. PATIENTS AND METHODS The study was conducted on 27 cases of cloaca that were managed at our unit during the last 12 years. Preoperative assessment included conventional investigations and MRI studies. Endoscopic and operative findings were important for confirmation and completion of the whole picture. For better perception of the degree of deviation from the norm, we included another control group of girls who underwent pelvic MRI studies for causes other than anorectal anomalies. RESULTS For practical reasons, we dissociated the cloacal complex into its two basic components to be described separately namely the anorectal anomaly and persistent urogenital sinus. The anorectal anomaly may be best described regarding two parameters: the position of the rectum and type of rectal communication with the urogenital tract. Persistent urogenital sinus anomalies were stratified based on referring the level of the urogenital confluence to the back of pubic symphysis. Three types could be identified (low, intermediate, and high) in which the mean length of the common channel was 6.4, 14.6, and 24 mm respectively with a significant statistical difference (Kruskal-Wallis chi-squared test). CONCLUSION Applying MRI in the preoperative assessment of cases of cloaca has the advantage of demonstrating the real anatomy of the anomaly in multiple planes. This can improve our perception of the degree of deviation from the norm in these cases, which may be important during planning for surgical reconstruction. LEVEL OF EVIDENCE This is a case control study (level III evidence).