The gastrointestinal tract is a dynamic ecosystem composed of an organized matrix of host eukaryotic cells, including a fully functional immune system, and numerous microbial habitats normally colonized by a diverse array of microbes. Recent analyses of the gastrointestinal microbiota by use of molecular-based methods indicate that bacterial populations vary substantially among but appear relatively stable within individuals. These observations raise many important questions about the role of the normal microbiota in the development of both the innate and the adaptive immune systems of the host and about how perturbations in this relationship may contribute to various intestinal or immunologic disorders. Here, 3 critical issues pertaining to the intestinal microbiota are briefly reviewed: what are the microbes, where are the microbes, and what controls the composition of the microbiota.