Complex female genitourinary system anomalies include a wide spectrum of uncommon pathologies, caused from the abnormal separation of the urorectal septum and the urogenital sinus in early embryonic life. The resulting fusion of the distal urinary, genital and intestinal tracts increases the risk of death in utero and alters the normal organ functionality and the quality of life in survivors. An accurate prenatal identification of these pathologies depends mainly on prior suspicion at ultrasound screening, but also requires a solid knowledge of embryology and familiarity with the different patterns of malformation. Prenatal MRI provides an excellent anatomic evaluation of the fetal anatomy that may improve the diagnosis in complex cases with inconclusive echographic findings. The additional information can help both families and medical teams to better evaluate the severity of the pathology and the postnatal prognosis and therefore to better orientate the management during pregnancy, at delivery and after birth. This review article describes the embryological basis and the clinical findings of the most relevant pathologies included in the spectrum. It also describes the imaging signs on prenatal MRI studies in a series of confirmed cases and proposes a diagnostic algorithm based on imaging findings for guiding prenatal diagnosis.