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The gut microbiota has been implicated in the pathogenesis and progression of kidney disease. However, little is known about the gut microbiota in hemodialysis (HD) patients. We assessed the gut microbiota and its relationship with clinical variables in 10 HD patients. We found that the Firmicutes-to-Bacteroidetes ratio was positively associated with traditional risk factors for cardiovascular disease. Furthermore, Faecalibacterium was positively associated with carbohydrate intake and negatively associated with arterial stiffness. Finally, endotoxemia was inversely associated with butyrate producers. Future studies should assess whether targeting the gut microbiota results in a lower burden for cardiovascular disease in HD patients.