Isolated congenital lymphoedema of the external genitalia in boys is extremely rare. It can have major physical and emotional consequences for the children. Three male patients with primary lymphoedema of the penis and scrotum are described. The first case presented with lymphoedema of the prepuce and the phallic skin that persisted after the age of 1 year. Circumcision and excision of the subcutaneous tissues of the phallic skin were successful in producing the appearance of a normal circumcised penis. The second case presented with oedema of both phallic and scrotal skin. At age 1 year only a pastous thickening of the prepuce remained, scrotal and phallic skin normalised spontaneously. Routine circumcision was successful with a 5-year follow up. The third case presented with persistent oedema of both the scrotum and the phallus. He suffered leakage of lymph requiring incontinence pads, with complicating skin infections recurring every 4-6 weeks at age 8 years. After complete peeling of the scrotal and phallic skin from subcutaneous tissue some leakage persisted, infections subsided. The cause of this disorder remains unknown, although hypoplasia of the lymphatic vessels is reported in most cases. In the literature, several congenital malformations have been associated with primary lymphoedema. These were not noted in our patients. Rarely, the lymphoedema regresses spontaneously. The treatment of persistent lymphoedema is surgical and consists of meticulous excision of all subcutaneous layers of the affected skin, combined with reconstruction of the penis and/or scrotum.Primary lymphoedema of the male external genitalia is an extremely rare malformation of the lymphatic vessels of unknown origin. If persistent, surgical treatment is necessary.