Children with anorectal malformations (ARM) constitute a significant group within a pediatric surgery practice. It is important with female cases of anorectal malformations to consider the association of gynecologic anomalies, especially at the time of the definitive repair. However, it is critical to consider the association of such gynecologic anomalies when caring for patients with a cloacal anomaly. If not recognized, an opportunity to diagnose and treat such anomalies may be missed with the possibility of negative implications for future reproductive capacity. With the knowledge of the associated anomalies and long term sequelae, surgeons can provide better care for girls and important counseling for parents. Knowledge of reproductive related issues in females with cloaca allows the pediatric surgeon an opportunity both, to provide optimal surgical management in infancy, childhood, and into young adulthood and to collaborate medically and surgically with an experienced gynecologist in patients with more complex anatomic variations. Appropriate counseling for patients and families about potential reproductive concerns that may develop many years after the definitive surgical repair allows preparation and planning to preserve future fertility.