Aims: Several studies have suggested that abnormalities in the small-intestinal microbiota might be involved in the development or the pathogenesis of celiac disease (CD). The objective of this study was to characterize and compare the composition of the duodenal microbiota between CD patients and non-CD controls. Method and Results: Bacterial communities were identified by pyrosequencing of 16S rRNA extracted from duodenal biopsies. The sequences analysis showed that the majority of the reads were classified within two phyla: Firmicutes and Proteobacteria. Bacterial richness and diversity were higher in non-CD controls than in untreated CD patients, but the differences were not statistically significant. The principal coordinates analysis revealed that bacterial communities of non-CD controls and untreated CD patients were dispersed without forming a clear group according to diagnosis of CD. Conclusions: There are no statistically significant differences in the upper small intestinal composition of bacterial communities between untreated CD patients and non-CD controls. Significance and Impact of the Study: This pyrosequencing analysis reveals a global picture of the duodenal microbiota that could be useful in future trials investigating the role of the microbiota in CD.