Abstract: Objective To compare the immunomodulatory effects of human amniotic mesenchymal stem cell (hAMSCs) and human bone marrow mesenchymal stem cells (hBMSCs) on peripheral blood T lymphocytes in an in vitro co-culture system. Methods hAMSCs and hBMSCs isolated using enzymatic digestion and Ficoll-Hypaque density gradient centrifugation, respectively, were culture-expanded in vitro to obtain the 4th-generation cells. The two MSCs were co-cultured separately with human peripheral blood mononuclear cells stimulated with phytohemagglutinin (PHA-PBMSC) to investigate the changes in T lymphocyte subsets using flow cytomety and the production of interleukin-2 (IL-2) and IL-10 by the T lymphocytes using enzyme-linked immunosorbent assay (ELISA). Results Co-culture with either hAMSCs or hBMSCs significantly increased the proportions of Treg, Th2 and Tc2 and decreased Th1 and Tc1 cell subsets in the PBMCs as compared with the PBMCs cultured alone (P<0.05), and the changes in the PBMCs were similar between the two co-culture systems (P>0.05). In both of the two co-culture systems, IL-2 production by the lymphocytes was significantly lowered (P<0.05) and IL-10 production was significantly increased (P<0.05) as compared with their levels in the PBMCs cultured alone; no significant difference was found in IL-2 or IL-10 levels between the two co-culture systems (P>0.05). Conclusion The MSCs derived from human amnion and bone marrow have similar immunomodulatory effects on the T lymphocytes, suggesting the possibility of using hAMSCs in the treatment of graft-versus-host disease after allogeneic hematopoietic stem cell transplantation.