Persistent urogenital sinus is frequently associated with a wide spectrum of complex anatomic abnormalities involving the urinary, genital, and gastrointestinal tracts. Failure to accurately define these abnormalities can result in serious complications. One such group of complications occurs relatively late in the clinical course of these children and has received little attention. These are the complications related to menarche. This report reviews the anatomy, complications, and management in five such patients. In this group the onset of menses was associated with hydrosalpinx, pyosalpinx, hematocolpos, hematometrocolpos tubo-ovarian abscess, ruptured ovarian endometrioma, endometriosis, and peritonitis. Anatomic abnormalities included double and septate vagina, vaginal atresia and stenosis, uterus didelphys, and uterus bicornis unicollis, all predisposing to inadequate menstrual flow. Each of these children required surgical intervention. These cases stress the need for an awareness of not only the urinary but the vaginal and uterine abnormalities. Careful early definition of the anatomy and long-term follow-up of children with urogenital sinus malformation is important in order to avoid potential future complications.