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Objective: To explore the mechanism of herb-partitioned moxibustion for ulcerative colitis (UC) through observing the colonic mucosal histopathological changes and the expression of nuclear factor kappaB (NF-kB) and peroxisome proliferators-activated receptorγ (PPARγ) mRNA of UC rats. Methods: Male SD rats were randomly divided into a normal group and a model group. UC model was established by general immunological plus local irritation method. After model identification, rats in the model group were randomly divided into a model group, a herb-partitioned moxibustion (HPM) group and a Western medicine (Salicylazosulfapyridine, SASP) group. Rats in the HPM group received treatment at bilateral Tianshu (ST 25) and Dachangshu (BL 25), two cones for each point, once a day for 7 d. SASP group rats were gavaged with SASP. The pathological scores were evaluated according to hematoxylin-eosin (HE) staining of colonic tissues. We used light microscopy to observe degree of colonic mucosal damage and the quantitative polymerase chain reaction (QPCR) to detect the expression of NF-κBp65 and PPARγ in colorectal mucosa. Results: Compared with the normal group, histopathological scores were significantly higher in the model group (P