thymic output was studied prospectively in 52 children who underwent allogeneic hematopoietic stem cell transplantation (allo-Hsct). thymic activity was assessed by quantification of recent thymic emigrants (rte) discriminated from the rest of naive t cells by immunophenotype cD3+/cD4+/ cD31+/cD45ra+. thymic output was analyzed in correlation with the kinetics of immune recovery and in relation to other potential risk factors that may influence thymopoiesis: underlying disease, type of Hsct, source of stem cells, age of recipient and donor, type of conditioning, implemented graft versus host disease (gvHD) prophylaxis, viral reactivations (herpes viruses cytomegalovirus-cMV, epstein-Barr virus-eBV, adenovirus-aDV, Bk virus-BkV), occurrence and grade of both acute and chronic graft versus host disease (agvHD, cgvHD) and number of transplanted cD34 cells/kg. the absolute count of rte in peripheral blood was evaluated at 6 time points: before the conditioning and on days +15, +30, +60 , +90 and +180 after Hsct. occurrence of grade ii-iV agvHD was the most important factor associated with low rte counts after Hsct. History of malignant disease, and transplantation from matched unrelated donor were risk factors for lower thymic output. we found a weak inverse correlation between the age of the recipient and thymic output on post-Hsct day +180. source of stem cells, type of conditioning, viral reactivations, occurrence of chronic gvHD, age of the donor and the number of transplanted cD34 cells/kg did not affect thymopoiesis in our study group. these preliminary findings and identification of risk factors for deterioration of thymic activity may in the future help in selecting candidates for thymus rejuvenation strategies.