Background: Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD) which highly affects the patients’ life quality with severe diarrhea and rectal bleeding. Relapsing inflammation in the mucosa of the colon due to immune imbalance can be the characteristic of UC. Unfortunately, until now, UC still cannot be completely cured. Clinically, 5-aminosalicylic acid (5-ASA), corticosteroids, immunomodulators and other biologic agents are used in the therapeutic treatment of this disease. However, the adverse effects limit the application of the drugs in the treatment of UC. Thus, it is necessary to find alternative therapies for the UC treatment. The herbs such as Scutellariae Radix (SR) and Radix et Rhizoma Rhei (Rhubarb), traditionally used for heat-dispersing and detoxification, have been prescribed as main component herbs for alleviating gastrointestinal disorders. Thus, the potential of applying the two herbs in UC therapies was evaluated in this study. Methods: The SR extract and the Rhubarb extract were prepared by water extraction and aqueous ethanol extraction, respectively, following the method documented in China Pharmacopoeia with minor modifications. Qualitative and quantitative analysis of flavonoids in SR extract and anthraquinones in Rhubarb extract were done using HPLC while the concentrations were calculated using the calibration curves. Twenty-four SPF grade Sprague-Dawley rats were randomly separated into four groups: Normal, UC, SR-treated and Rhubarb-treated group. The induction of UC was prepared by giving the rats 5% DSS in drinking water for 7 days. For the treatment groups, 1g/kg SR extract or 1.5g/kg rhubarb extract was administered orally once a day for 7 days. At the end of the experiment, animals were sacrificed and blood samples, small intestine and colon samples were collected for macroscopic assessment, histological examination and biochemical assessment to evaluate the therapeutic effects of SR and Rhubarb in the treatment of UC. iv Results: The extraction methods were established to prepare SR and Rhubarb extracts and the main components flavonoids and anthraquinones were determined qualitatively and quantitatively using HPLC plus authentic compounds. In the in vivo study, DSSinduced animals exhibited UC-like symptoms (diarrhea, occult blood in stools and weight loss) and immune imbalance (significantly increase in production of proinflammatory cytokines and decrease in production of anti-inflammatory cytokines). For the treatment groups, SR reduced body weight loss, lowered the DAI and partially alleviated the symptoms of UC at later treatment period, while Rhubarb extract exacerbated the UC-like symptoms. Both SR and Rhubarb reduced the myeloperoxidase (MPO) activity in colon mucosa and exhibited management in the level of inflammatory cytokines and chemokines in serum and colon by increasing the level of anti-inflammatory cytokines and decreasing the level of pro-inflammatory cytokines. Conclusions: In this preliminary study, both SR and Rhubarb showed efficacy to balance the inflammatory immune system, but only SR exhibited alleviation to the symptoms in the experimental colitis rats. Further studies are warranted to systematically assess the efficacy and safety of SR in the treatment of UC.