Female genital tract malformations are frequently a cause of reproductive problems. Besides, complex malformations also frequently generate serious gynecological problems, often ones with inappropriate surgical solutions, as the gynecologist does not think of the malformation as either the cause of the symptoms or of its embryonary origin. Apart from analyzing the embryological bases in the development of the female genital tract and insisting on the well known müllerian origin of the uterus, the ratification of the embryological hypothesis about the origin of the human vagina from the Wolff ducts and the Müller tubercle allows us to not only advance in knowledge but to use that knowledge for better clinical management of the problems generated by the complex malformations of the female genital tract. In this review we study the methods and means for the diagnosis of female genital-urinary malformations, their classification and clinical findings, and especially those cases involving unilateral renal agenesis, vaginal ectopic ureter and other complex malformations. We also analyze the related obstetric and gynecologic pathology, and especially that cases of complex genital malformations. We review the related literature and some interesting case reports, as well as our experimental studies in rats. After re-asserting our hypothesis about the embryology of the human vagina as derived from the Wolff ducts and the Müller tubercle, we suggest different recommendations for a better approach and management of the malformations of the female genital tract according to the findings observed in different diagnostic procedures.