PURPOSE OF REVIEW: To review the current knowledge of the connections between the innate and adaptive immune systems in the etiology and pathogenesis of inflammatory bowel disease (IBD). RECENT FINDINGS: Immune homeostasis in the mammalian intestine balances colonization by a symbiotic microbial flora and host defense. IBD is thought to be a breakdown of this balance. Although early studies shed light on the role of the adaptive immune system and negative regulators of homeostasis in IBD pathogenesis, here we review recent findings on the role of the innate immune system and microbial symbionts in the development of IBD. SUMMARY: Both the inflammatory and immune responses may be characterized according to modules of initiators, triggers, mediators and effectors. Use of this framework may guide our understanding of disease pathogenesis. Here we apply this model to the pathogenesis of IBD.