The embryological development of the male urinary system remains a subject of much controversy. As a result the pathogenesis of congenital anomalies such as hypospadias and epispadias, which are presented to the reconstructive surgeon remains poorly understood. A review of the literature identifies its three principal developmental stages: (1) division of the cloaca into the urogenital sinus and hindgut by the urorectal septum and the formation of the perineum; (2) the extension of the cloaca and its epithelium in the form of the urethral plate through the developing genital tubercle; (3) the separation of this extension from the surface during the formation of the urethra. This study, which uses a mouse model, examines these developmental stages in detail and together with a comprehensive review of the literature resolves many of the controversies relating to the development of the male urinary system. It reveals new insights into the origin of the associated congenital defects.