Female long term survivors of allogeneic hematopoietic stem cell transplantation incur a significant burden of late effects. Genital GVHD, HPV reactivation, ovarian failure and infertility, sexual dysfunction and osteoporosis are concerns that can significantly impact quality of life. This review examines the risk, pathogenesis, clinical presentation and implications of these common complications. Recommendations are provided for evaluation and management of these late effects, and other obstetric and gynecologic issues that may arise in this patient population.