The small intestinal microbiota plays a crucial role in maintaining the health and pathogenesis of various gastrointestinal disorders. Despite extensive research on gut microbiota, studies focusing on the small intestine are limited owing to methodological challenges. This review discusses the taxonomic composition, microbial load, and diversity of normal small intestinal microbiota. Additionally, it highlights the role of small intestinal microbiota in gastrointestinal disorders, such as functional dyspepsia, small intestinal bacterial overgrowth, and nonsteroidal anti-inflammatory drug-induced enteropathy. The impact of proton pump inhibitors on small intestinal microbiota dysbiosis underscores the importance of the appropriate use of strong acid suppressants in clinical practice. Future research should focus on both the luminal and mucosal microbiota of the small intestine to explore the taxonomic changes and functional differences.