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Background: Several recent studies have reported the relationship between atherosclerosis and gut microbial imbalance. Small intestinal bacterial overgrowth (SIBO) is one of the most common forms of gut microbiota imbalance, and studies have shown that SIBO plays an important role in human health. However, the relationship between SIBO and subclinical atheromatous plaques remains unclear. The aim of this study was to investigate the frequency of subclinical atheromatous plaques in patients with SIBO and to explore the association between these two conditions. Methods: A total of 411 eligible subjects were included in this study. The lactulose hydrogen-methane breath test was used to diagnose SIBO, and ultrasound examinations of the carotid, abdominal aorta and lower extremity arteries were performed in all subjects to assess the presence of plaques. Results: Plaques were more common in the SIBO-positive group than in the SIBO-negative group (abdominal aorta, 74.2% vs. 38.8%, p < 0.01; carotid arteries, 71.7% vs. 52.3, p < 0.01; lower extremity arteries, 73.4% vs. 57.6%, p < 0.01). After adjusting for traditional confounders, compared to the SIBO-negative population, the SIBO-positive population had, respectively, OR = 4.18 (95% CI = 2.56–6.80, p < 0.001), OR = 1.93 (95% CI = 1.23–3.02, p = 0.004), OR = 1.81 (95% CI = 1.14–2.88, p = 0.011) and OR = 5.42 (95% CI = 2.78–10.58, p < 0.001) for abdominal, carotid, lower extremity and any-territory plaque presence. Conclusion: SIBO was found to be associated with subclinical atheromatous plaques, and the mechanism of this association warrants further exploration. [ABSTRACT FROM AUTHOR]