Analysis of cytokine gene expression in peripheral blood mononuclear cells from patients received allogeneic hematopoietic stem cells transplantation (allo-SCT) showed that type 1 helper T cells (Th1)-derived cytokines increased in severe graft-versus-host disease (GVHD) while Th2-derived cytokines such as IL-4, IL-10, and IL-13 increased in mild GVHD. These results indicate that Th2 cells suppress GVHD although Thl cells augment GVHD. Chimerism analysis showed that mixed chimerism was often observed in younger (<30 years old) patients. Mixed chimerism in older (> or = 30 years old) patients were related to rejection and relapse while this situation is not the case in younger patients, thus indicating that mixed chimerism is an important prognostic factor in older patients. Among the chimerism of various cell populations, donor-derived CD56-positive cells are important in early engraftment when determined in allogeneic nonmyeloablative stem cell transplantation (allo-NST), regardless of the proportion of donor-derived CD3-positive cells. This result suggests that donor-derived CD56-positive cells are a more useful indicator for engraftment and rejection in early time period. Complementary-determining region 3 (CDR3) size spectratyping in T-cell receptor (TCR) chain subfamilies (V beta) showed that high level of diversity in TCR V beta repertoire is important for a late rejection and skewed TCR V repertoire is well correlated to occurrence of GVHD. Expression of inhibitory natural killer (NK) cell receptors such as CD158b and CD94/NKG2A on peripheral CD3-negative and positive cells were increased in parallel with GVHD. Interestingly, these molecules appeared to regulate GVHD while preserving graft-versus-leukemia (GVL) effect.