To help physicians and radiologists in the diagnosis of female genito-urinary malformations, especially of complex cases, the embryology of the female genital tract, the basis for Müllerian development anomalies, the current classifications for such anomalies and the comparison for inclusion and cataloguing of female genital malformations are briefly reviewed. The use of the embryological system to catalogue female genito-urinary malformations may ultimately be more useful in correlations with clinical presentations and in helping with the appropriate diagnosis and treatment. Diagnostic imaging of the different genito-urinary anomalies are exposed, placing particular emphasis on the anomalies within group II of the embryological and clinical classification (distal mesonephric anomalies), all of them associated with unilateral renal agenesis or dysplasia. Similarly, emphasis is placed on cases of cervico-vaginal agenesis, cavitated noncommunicated uterine horns, and cloacal and urogenital sinus anomalies and malformative combinations, all of them complex malformations. Diagnostic imaging for all these anomalies is essential. The best imaging tools and when to evaluate for other anomalies are also analysed in this review.Teaching points• The appropriate cataloguing of female genital malformations is controversial.• An embryological classification system suggests the best diagnosis and appropriate management.• The anomalies most frequently diagnosed incorrectly are the distal mesonephric anomalies (DMAs).• DMAs are associated with unilateral renal agenesis or renal dysplasia with ectopic ureter.• We analyse other complex malformations. Diagnostic imaging for these anomalies is essential.