The intestine is normally colonized by a large and diverse commensal microbiota and is occasionally exposed to a variety of potential pathogens. In recent years, there has been substantial progress made in identifying molecular mechanisms that normally serve to protect the intestine from such enteric bacteria and which may go awry in chronic idiopathic inflammatory diseases of the gut. One specific molecular interaction that appears to play a key role in governing bacterial-intestinal interactions is that of the bacterial protein flagellin with toll-like receptor 5. This article reviews studies performed in vitro, in mice, and in humans that indicate an important role for the flagellin-TLR5 interaction in regulating both the innate and adaptive immune responses in the intestine.