Allogeneic hematopoietic stem cell transplantation (allo-HSCT) nowadays allows cure malignant and nonmalignant diseases considered to be fatal previously. The number of cancer survivors' children progressively increases over years. Unfortunately, numerous late effects of allo-HSCT become both a serious problem and a cause of the morbidity and mortality. Among them the reproductive pathology seems to be frequent, and fertility problems influence the quality of life of patients significantly. Material and methods. We present the results of the evaluation of reproductive system in 294 children after allo-HSCT. Reproductive problems were revealed in 43 children and adolescents (15% of all patients and 46% of the patients with endocrine pathology). Hypergonadotropic hypogonadism was the dominating problem (33 patients, 77% of all reproductive dysfunctions). Results. Risk factors of its development included: busulfan-containing conditioning regimen (p < 0.001, risk ratio (RR) of hypogonadism was 26.7% compared to 5.2% in other regimens), diagnosis of the malignant disease (p = 0.002, RR 26.6% in malignant and only 8.1% in nonmalignant pathology), central nervous system irradiation prior to HSCT (p = 0.002, RR 32.6% with cranial irradiation compared to 15.6% without it), female gender (p = 0.003, RR increases up to 3 times - 26.9% in girls against 9.3% in boys). We also describe cases of the fertility restoration and birthgiving. The algorithm of diagnostic and follow-up of gonadal pathology in children after allo-HSCT is shown.