In women after hematopoietic stem cell transplantation (HSCT), complications associated with the original disease and therapies used both before and after transplantation often occur, which significantly affects their quality of life. The most common gynaecological complications include secondary cancers, premature ovarian insufficiency (POI), infertility and chronic graft-versus-host disease (cGVHD). Cervical cancer is the most common secondary genital cancer in patients after HSCT. Regular screening and vaccination against HPV (Human Papillomavirus) can significantly reduce the risk for its occurrence. The specific complication after allogeneic hematopoietic stem cell transplantation is graft-versus-host disease (GVHD), the genital form of which can lead to labial and vaginal adhesions, significantly reducing the women's quality of life. The basis of treatment is local steroid therapy and immunosuppression. A consequence of chemotherapy and radiation therapy may be damage to the gonads leading to premature ovarian insufficiency and the onset of menopause symptoms. The basis of treatment is systemic hormone therapy used until middle age when natural menopause is reached. Women after HSCT who are of reproductive age also suffer from infertility. An important role of the doctor is to educate patients about the risk for infertility and to suggest appropriate methods of preserving fertility before starting treatment. The recommended procedure for fertility preservation is cryopreservation of embryos or oocytes. The freezing and retransplantation of ovarian tissue is becoming an increasingly popular method of fertility protection. Preventive examinations and early detection and treatment of gynaecological complications significantly improve the comfort of life and health of women after HSCT.