The role of intestinal bacteria in the pathogenesis of nonalcoholic fatty liver disease is increasingly acknowledged. Recently developed microbial profiling techniques are beginning to shed light on the nature of gut microbiota alterations in nonalcoholic fatty liver disease. In this review, we summarize the gut microbiota composition changes that have been reported during different stages of human nonalcoholic fatty liver disease, and highlight the relation between bile acids and gut bacteria in this context. In addition, we discuss the different methodologies used in microbiota analyses as well as the interpretation of microbiota data. Whereas the currently available studies have provided useful information, future large-scale prospective studies with carefully phenotyped subjects and sequential sampling will be required to demonstrate a causal role of gut microbiota changes in the etiology of nonalcoholic fatty liver disease.