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The biological features of intrahepatic CD4+ CD25+ T regulatory cells in the naturally tolerance of rat liver transplantation were explored. Orthotopic liver transplantation was performed in two allogeneic rat strain combinations, one with fatal immunosuppression despite a complete major histocompatibility complex mismatch. The subjects were divided into three groups according to different donors and recipients [Tolerance group: LEW-to-DA; Rejection group: DA-to-LEW; Syngegnic group (control group): DA-to-DA]. The proportion of intrahepatic CD4+CD25+ T cells from three groups was determined by flow cytometry (FCM) in different time. The intrahepatic CD4+CD25+ T cells were isolated by magnetic activated cell sorting (MACS) method and identified by FCM. The Foxp3 mRNA was detected by reverse transcriptase polymerase chain reaction (RT-PCR). And their suppression on the proliferation of CD4+CD25− T effector cells was analyzed by cell proliferation assay in vitro. Beginning immediately after transplantation, the proportion of Treg cells increased over time in both allogeneic groups but was significantly greater in the Rejection group. The proportion of Treg cells declined after day 5, and such reduction was more dramatic in the Rejection group than in the Tolerance group. Animals in the Tolerance group showed a second increase in the proportion after day 14. Intrahepatic CD4+ CD25+ T cells isolated from spontaneous tolerance models inhibited the proliferation of mixed lymphocyte reaction. The purity of CD4+CD25+ T cells sorted by MACS was 86%–93%. The CD4+CD25+ T cells could specifically express the Foxp3 gene compared with CD4+CD25− T cells. In vitro, the spleen cells from LEW rats can irritate the proliferation of CD4+CD25+ T cells more obviously than the syngegnic spleen cells. CD4+CD25+ Tr cells could suppress the proliferation of CD4+CD25− T cells, but the inhibition was reversed by exogenous IL-2 (200 U/mL). The CD4+CD25+ T regulatory cells specifically express the Foxp3 gene, which may play an important role in the induction of liver transplantation tolerance by suppressing the reaction of effective T cells. [ABSTRACT FROM AUTHOR]