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We aimed to develop a new diagnostic method for colorectal cancer by analysing the protein profiles of extracellular vesicles in faeces. Enrichment analysis of proteomic data on extracellular vesicles highly purified from faeces by density gradient centrifugation revealed that proteins detected only in extracellular vesicles were significantly enriched in proteins derived from the colon. Notably, proteins detected only in faecal suspensions showed no enrichment in colon-derived proteins, suggesting that faecal extracellular vesicles can be used to detect changes in the protein profile that occur in the colon. In addition, we identified four candidate biomarkers among the proteins that were altered in the faecal extracellular vesicles of patients with colorectal cancer identified by proteomic analysis. By comparing different healthy control samples, olfactomedin-4 (OLFM4) and galectin-3-binding protein (LGALS3BP) in faecal extracellular vesicles were significantly increased in patients with colorectal cancer. This study shows that faecal extracellular vesicles are a promising biomarker resource for colorectal diseases, including colorectal cancers. 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