Objective To investigate the impact of bone marrow mesenchymal stem cell transplantation on a rat model of experimental autoimmune uveitis (EAU) and analyze its immune regulatory mechanisms in vivo.Methods Eighteen Lewis rats were randomly divided into three groups: model control group, intervention group and normal control group, six animals in each group. Human retinal S-antigen peptide (HS-AgP35, 1 mg/ml) was mixed and emulsified with complete Freundprime;s adjuvant and injected into hind foot pad of rats on the first and eighth day to establish the animal model of EAU. For bone marrow mesenchymal stem cell transplantation, 1 ml of cell suspension (2times;106 cells/ml) was injected into tail vein of the intervention group rats on the first day when the emulsified S-antigen was injected. EAU manifestation, pathological change and IFN-gamma; level were evaluated and compared among those three groups after two weeks. Results No abnormal signs were found in the eyes of rats in normal control group. The manifestation grading of the intervention group (two rats at grade 0, three rats at grade 0.5, one rat at grade one) was significantly different from the model control group (one rat at grade one, one rat at grade two, three rats at grade three, one rat at grade four) (P=0.015). The retina of rats in normal control group was ordinary under light microscope. The histopathologrical grading of the intervention group (one rat at grade 0, four rats at grade 0.5,one rat at grade one) and the model control group (four rats at grade three, two rats at grade four) was also statistically different (P＜0.01). Furthermore, the IFN-gamma; level in peripheral blood of the intervention group rats declined significantly compared to the model control group (t=9.0574, P=0.01). Conclusions Bone marrow mesenchymal stem cells can inhibit EAU significantly, possibly by lowering the level of IFN－gamma;, thereby reduce the severity of uveitis and improve the condition of uveitis in rats.