Background: The protective effect of the chloroform extract of Cyperus rotundus (CHCR) is attributed to its anti-inflammatory and antioxidant activities. Cytokines, important regulators of inflammation and repair, play a key role in the pathogenesis of inflammatory bowel disease (IBD). Targeting these cytokines can effectively ameliorate the symptoms of IBD. The aim of the present study was to unravel the molecular mechanism through cytokine regulation in rats in experimental IBD.Methods: Sprague Dawley rats were randomly allocated to 5 groups (n=6). Group I served as the normal control. Group II served as the vehicle control and received 50% ethanol intracolonically on day 11 of the study. Group III served as the model control. Group IV and Group V were given standard drug 5-aminosalicylic acid (100 mg/kg) and CHCR (800 mg/kg), respectively, for 18 days once a day orally. Colitis was induced with dinitrobenzene sulfonic acid (180 mg/kg in 50% ethanol) intracolonically in groups III–V on day 11 of the study. On day 18, the rats were euthanized and colon tissues were removed for IL-4, IL-6, IL-12, and IFN-gamma gene expression studies using quantitative RT-PCR.Results: The expression levels of proinflammatory cytokines IL-4, IL-6, IL-12, and IFN-gamma were upregulated in the model control rats. Pretreatment with 5-aminosalicylic acid (100 mg/kg) and CHCR (800 mg/kg) significantly decreased the fold of the expression of the above cytokines.Conclusion: CHCR acts as a molecular brake and downregulates the expression of proinflammatory cytokine genes; this is beneficial for reducing the severity of the experimental IBD. Thus, Cyperus rotundus is a safe, economical, and effective alternative for the treatment of patients with IBD.