To determine the expression of NF-κBp65 and STAT6mRNA prior to and after acupoint embedment treatment in rats with TNBS induced colonitis, and to investigate mechanism of action of the treatment. Methods:The male rats (n=18) were randomized to normal group, model group and treatment group. The model was established using TNBS. The model group received no intervention, and was on normal diet. acupoint embedment treatment. On D15 the histopathology of colon was observed, NF-κBp65 expression was determined by western blot, and STAT6mRNA expression was determined by RT-PCR. Results:The treatment group recovered more fast from diarrhea and bloody purulent stool, and mucous membrane injury was significantly improved. Compared with the normal group, the model group had significantly higher expression of NF-κBp65 and STAT6mRNA (P<0.01), while the treatment group had significantly lower expression (P<0.01).Conclusion:The effectiveness of acupoint embedment treatment is achieved by down regulation of inflammatory factor through NF-κBp65, STAT6mRNA.