Thymidine ((3)H-TdR) incorporation remains the most commonly used method to quantifying T-cell proliferation. This method, however, does not provide information about specific lymphocyte subpopulations responding to different stimuli. In our study, we modified previously described nonradioactive flow-cytometric T-cell activation assay measuring the expression of a CD69+ antigen on T-cell subsets and applied it to analysis of lymphocyte subsets activation/proliferation in children after allogeneic hematopoietic cell transplantation (HCT). We compared the percentage of spontaneously activated lymphocyte subpopulations (background) and the percentage of PHA-P, PWM, and SEB-stimulated cell subsets from two groups of patients: group 1, children with Graft versus Host Disease (GvHD) and group 2, children without any signs of GvHD at the time of analysis. High rate of spontaneous T-cell subset activation was found in group 1 with CD3+CD8+Ts cells being the most affected cell population. High background activation of Th and B cells correlated with the occurrence of autoimmune phenomena posttransplant. Rapid quantification of CD69+ expression on unstimulated and stimulated T-cell subsets proved to be a valuable method for monitoring children after allogeneic HCT. High proportion of activated, unstimulated Ts cells observed in the GvHD group may underline the critical role of CD3+CD8+ cells in the pathogenesis of GvHD. Thus in future immunosuppressive therapy may be adjusted according to the proportion of activated Ts cells.