Alterations in the diversity of the gut microbiota are believed to underlie the development of antibiotic-associated diarrhea (AAD). A molecular phylogenetic analysis was performed to document temporal changes in the diversity of fecal bacteria of a patient who developed AAD. Antibiotic administration was associated with distinct changes in the diversity of the gut microbiota, including a marked decrease in the prevalence of butyrate-producing bacteria. Following the discontinuation of the antibiotic, resolution of diarrhea was accompanied by a reversal of these changes, providing the first direct evidence linking changes in the community structure of the gastrointestinal bacteria with the development of AAD.