Molecular and immunologic mechanisms underlying inflammation in inflammatory bowel disease (IBD) are largely unknown. Recent studies have helped better characterize genetic and environmental factors associated with colitis. Discoveries of genetic variants have confirmed that IBD is a bacteria and cytokine-driven pathologic immune response. Data have demonstrated that certain T cell subsets are important in executing the inflammatory cascade. Insufficient regulatory cell activity or modulatory cytokine production results in unrestrained inflammation. Biologic agents that block inflammatory cytokines (anti-TNFalpha antibodies) have been used successfully to treat IBD. Recent advances have also identified mucosal regulatory pathways.