We studied gonadal function in 42 girls who underwent stem cell transplantation (SCT) between 1982 and 1997. Their median age at the time of transplantation was 11 years (range: 5 to 16 years), and that at the time of the study was 17 years (range: 13 to 27 years). Diagnoses included acute leukemia (n=25), aplastic anemia (n=12), chronic myelogenous leukemia (n=3) and lymphoma (n=2). They were assigned to one of four groups according to the preconditioning regimen used for SCT; busulfan plus melphalan (BU group; n=17), high-dose chemotherapy plus total body irradiation (TBI group; n=15), cyclophosphamide plus total lymphoid irradiation (TLI group; n=7), and all others (n=3). Gonadal function was assessed by occurrence of menstruation, serum levels of LH, FSH, and estradiol (E₂). Twenty-eight of forty-two patients (67%) had no menstruation after SCT. The percentages of patients with amenorrhea were 100%, 60% and 14% in the BU, TBI and TLI groups, respectively. These findings confirm that a busulfan plus melphalan regimen is a major risk factor for ovarian dysfunction in children after SCT.