BACKGROUND: There are many factors associated with chronic pain, including changes in the nervous and musculoskeletal systems and so on. Recently, it has become clear that the gut microbiota (GM) influences these factors, and there are many reports of GM dysbiosis in patients with chronic pain. However, the relationship between pain and GM remains unclear. Our previous study reported that defecation status, which reflects GM composition, was associated with pain intensity and that this relationship was different for each pain site. Our study investigated the association between pain site and the GM composition of feces in chronic pain patients. METHODS: The subjects were 136 patients with chronic pain and 125 healthy controls. Patients were classified into four groups, whole body (WB) pain, lower back and lower extremity (LL) pain, headache, and upper back and upper extremity pain, based on the site of pain, and we investigated differences in GM taxonomy groups compared with healthy subject. RESULTS: Chronic pain patients had a lower alpha diversity (effect size=0.16, p=0.02). But each pain site group did not differ in alpha diversity. WB pain patients showed higher Eggerthellaceae (LDA=3.09, p<0.01) and lower Halomonas (LDA =-2.72, p<0.01). LL pain patients had increased Fusobacterium and Sellimonas (LDA=4.09,3.03 p<0.01, 0.01) but reduced Halomonas (LDA=-2.59, p<0.01), and other key taxa. CONCLUSION: WB and LL patients may have GM compositions different from healthy controls, but larger studies are needed to confirm this.