Objectives. To assess the value of magnetic resonance imaging (MRI) in the anatomic evaluation and management planning of complex congenital genitourinary anomalies. Methods: Multiplanar T 1 and T 2-weighted MR images were obtained in 6 pediatric patients with congenital genitourinary anomalies, including aphallia, diphallia, ectopic scrotum, and epispadias. The imaging studies were read by experienced radiologists and discussed with the urologic surgeons in a multidisciplinary conference. Results. Each congenital anomaly was demonstrated in detail by MRI. The MR images of penile agenesis showed hypoplastic corpora cavernosa and a vestigial bulb. In patients with penile duplication, MRI was able to delineate the course of each corporal body and the varying degree of thickness of the tunica albuginea. For the patient with scrotal ectopia, detailed MR images excluded both the possibility of urethral and corporal duplications and the presence of viable testes in the ectopic scrotum. In the case of epispadias, MRI illustrated the precise spatial relationship between the erectile bodies and urethra. Additionally, MRI identified related aberrant pelvic organs and provided images of the external genital structures. Conclusions. MRI, by rendering excellent anatomic interpretation of complex genital anomalies and associated abnormal pelvic tissues, assists surgeons in conceptualizing the anomalous structures and contributes to their formulation of management approaches.