Advances in our understanding of the complex, dynamic interactions that exist among the gastrointestinal microflora, the epithelium of the gastrointestinal mucosae, and the immune system have been facilitated by powerful new genetic tools. Recent understanding that the gastrointestinal epithelium performs not only a barrier function but is also an active sensor of the microflora and an important intermediary in regulating and integrating cross-talk between it and cells of the innate and adaptive immune systems provides one of the most fertile and challenging areas for application of these technologies. The intestinal epithelium also represents an important model system for study of programs of cell lineage commitment and differentiation, given its continual and rapid regeneration throughout life and the regional differences in these programs that exist along the gastrocolonic and crypt-villous axes. This review will highlight current and emerging technologies that are available in the mouse model for identification and manipulation of genetic elements that regulate the normal and pathological physiology of the intestinal tissues in the postgenomic era.