To study the changes of CD4(+)CD25(+) and CD8(+)CD103(+) regulatory T cells and their relevant cytokines in corneal allograft transplantation in mice. BABL/c (H-2(d)) mice received corneal allografts from C3H/He (H-2(k)) mice were served as the experimental group. BABL/c (H-2(d)) mice received corneal from BABL/c (H-2(d)) mice were used as the control group. Corneal graft survival time was recorded pre-, 3rd day, 7th day, 4th week, 8th week post-operatively. Infiltration of inflammatory cells and corneal neovascularization were evaluated by histopathologic examination. The percentage of CD4(+)CD25(+) and CD8(+)CD103(+) T cell in peripheral blood and spleen was determined by flow cytometry. The expression of interleukin-10 (IL-10), IL-4, gamma-interferon (IFN-gamma) and IL-1beta in serum and aqueous humor was measured by enzyme-linked immunospecific assay (ELISA). The graft rejection in experimental group occurred at 7 days to 4 weeks after the operation, averaged (14.79 +/- 1.02) days. The grafts in the control group remained clear within 8 weeks observation and the survival time is much longer than that of the allografts (chi(2) = 46.934, P = 0.000). Flow cytometry showed that the percentage of CD4(+)CD25(+) T cell in peripheral blood in the control group after surgery was (3.36 +/- 0.29)%, (4.09 +/- 0.44)%, (5.44 +/- 0.35)%, (5.73 +/- 0.53)% at day 3, day 7, 4th week, and 8th week, respectively, which was significantly higher than that in the experimental group [(2.50 +/- 0.39)%, (3.24 +/- 0.25)%, (4.20 +/- 0.45)%, (4.18 +/- 0.14)%; t = 3.828, 2.898, 3.780, 4.892; P < 0.05]. On the other hand, CD8(+)CD103(+) T cell in peripheral blood in the experimental group after surgery was (2.20 +/- 0.33)%, (2.79 +/- 0.57)%, (4.55 +/- 1.03)%, (4.31 +/- 0.07)% at different periods, which was much higher than that in the control group (t = 7.133, 4.876, 5.196, 19.960; P < 0.05). The changes of CD4(+)CD25(+) and CD8(+)CD103(+) T cells in the spleen was earlier than those in peripheral blood. ELISA showed the expression of IL-10 and IL-4 in the serum in experimental group after surgery was much lower than that in the control group (t = 3.203, 3.141, 3.012, 2.869 and 2.340, 6.681, 8.839, 8.574; P = 0.011, 0.012, 0.013, 0.019 and 0.053, 0.000, 0.000, 0.000). The serum levels of IFN-gamma and IL-1beta in experimental group were higher than that in the control group (t = 3.508, 3.265, 4.402, 5.539 and 3.630, 5.796, 1.728, 0.660; P = 0.006, 0.011, 0.002, 0.000 and 0.005, 0.000, 0.115, 0.524). Furthermore, the cytokine levels in the aqueous humor behaved similarly with those in the serum. The down-regulation of CD4(+)CD25(+) Treg, IL-10 and IL-4 and the up-regulation of CD8(+)CD103(+) Treg, IFN-gamma and IL-1beta in mice allograft corneal rejection may play an important role in allograft rejection.