CD46 is not only identified as a complement regulatory protein which protects host cells from complement attack, but also a new co-stimulatory molecule for human T cells. CD3/CD46 co-stimulation can induce a T-regulatory 1 cell (Tr1)-specific cytokine phenotype in human CD4(+) T cells. However, the role of CD46 as a co-stimulatory molecule in the modulation of the acquired immunity, such as transplant immunology, remains unclear. In this study, CD4(+) T cells were isolated from human CD46-transgenic C57BL/6 mice by magnetic-activated cell sorting, and further induced by anti-CD3, anti-CD28 and anti-CD46 antibodies respectively, and anti-CD3/anti-CD28 antibodies, anti-CD3/anti-CD46 antibodies, or the monoclonal antibody panel against CD3/CD28/CD46. The levels of interleukin-2 (IL-2), gamma-interferon (gamma-IFN), interleukin-10 (IL-10) and transforming growth factor-beta (TGF-beta) were detected in the supernatants of different groups. Suppression of allogeneic T cell proliferation were assessed by using mixed lymphocyte reaction (MLR) assay, in which monoclonal antibodies against CD46 were added to the culture. The results showed that CD3/CD28, CD3/CD46 and CD3/CD28/CD46 co-stimulation could significantly induce stronger proliferation of T cells than CD3 stimulation (P<0.05), and CD3/CD28/CD46 co-stimulation significantly increased the proliferation of T cells when compared with CD3/CD28 or CD3/CD46 co-stimulation (P<0.05 for each). IL-2 and gamma-IFN levels were much higher in CD3/CD28 co-stimulation group than in CD3, CD28, CD46 and CD3/CD46 groups (P<0.05 for each). IL-10 and TGF-beta levels were dramatically increased in CD3/CD46 co-stimulation group as compared with those in the CD3, CD28, CD46 and CD3/CD28 groups (P<0.05 for each). CD3/CD46 co-stimulation significantly inhibited the T cell proliferation and allogenic immune responses through the secretion of IL-10 and TGF-beta in MLR (P<0.05). These results suggested that CD3/CD46 can induce Tr1 cells to modulate allogenic immune responses, and it may become a novel target for the development of new therapeutic approach for T-cell-mediated diseases. CD46 plays an important role in regulating the T cell-mediated immune responses by bridging innate and acquired immunity.