We co-exist in harmony with huge numbers of bacteria, many within our own gastrointestinal (GI) tracts. On occasion, however, particularly virulent bacteria called pathogens (Salmonella, EHEC O157:H7) infect our intestines and cause severe, even fatal, disease. To fight infections, our immune system must recognize these bacteria as harmful and trigger a protective immune response. Some individuals appear highly susceptible to infections, perhaps because their immune systems are unable to recognize or effectively deal with the bacteria. Inappropriate recognition of pathogens may also contribute to chronic diseases of the GI tract such as Crohn's disease and other inflammatory bowel diseases (IBD). We believe that in IBD an individual’s immune system mistakes harmless bacteria for pathogens and attacks them, causing chronic inflammation. Using immunological and microbiological techniques, we’re learning how our immune systems recognize bacteria in the GI tract. We’re also identifying the factors that can provide resistance or susceptibility to intestinal infections, and exploring the mechanisms underlying the dysfunctional pathogen recognition that can trigger chronic IBD.