The human intestinal microbiota is a complex bacterial consortium that is critical to normal health. The microflora is present at concentrations of 10(11)-10(12) cells/g of intestinal contents; the number of species present may exceed 500, although exact numbers remain to be defined, due in part to the fact that <30% of microorganisms are culturable with current microbiologic methods. Molecular tools based on 16S rDNA sequence similarities such as fluorescent in-situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), quantitative dot blot hybridization, restriction fragment length polymorphism (RFLP) and large scale 16S rDNA sequencing have helped to overcome limitations of conventional microbiological plating methods in studying the fecal microflora composition. However, these tools are just now beginning to be applied to understand the dynamics of this complex community, and its relationship to diet and human health. There is a need to understand both the limitations of the current data and the importance of moving forward with the best possible molecular and epidemiologic techniques as we deal with these critical questions.