To assess the kinetics of lymphocyte subset recovery, 758 allografted patients were monitored by surface markers (CD3, CD4, CD8, CD56), with a 5-year follow-up. The donor was a matched sibling donor (MSD) (n ¼ 502) or an alternative donor (family mismatched or unrelated, AD) (n ¼ 256). The stem cell source was bone marrow for all patients. CD4 þ cell recovery was influenced-in univariate analysis-by three factors: donor type, patient age and GvHD. This was not the case for CD8 þ and CD56 þ cells. The median CD4 þ cell count on day þ 35 after HSCT was 86/ll. Patients achieving this CD4 þ cell count had significantly lower transplant-related mortality (TRM) compared to patients who did not achieve this CD4 þ cell count (20 vs 39%, P ¼ 0.00001), due to a lower risk of lethal infections (24 vs 47%, P ¼ 0.0003). In multivariate analysis MSD (RR 3.45, P ¼ 0.0001) and recipient age less than 16 years (RR 3.23, P ¼ 0.003) were significantly associated with a better CD4 þ cell recovery. CD4 þ counts on day þ 35 was predicted TRM (RR ¼ 1.97, P ¼ 0.0017) together with acute GvHD grade II-IV (RR 1.59, P ¼ 0.0097). No difference of TRM was observed for CD8 þ and CD56 þ cell counts.