The study examined the association between the ratio of visceral (inner abdominal) to subcutaneous fat (VSR) and the risk of gallstones in 4,914 Korean men. Fat areas were measured using computed tomography (CT) at the L3 vertebral level, and participants were divided into four groups according to VSR. The results showed that the prevalence of gallstones increased with increasing VSR, from 4.0% in the lowest quartile to 7.6% in the highest (p < 0.001). After adjustment for age, BMI, lifestyle, comorbidities and biochemical markers, men in the highest quartile of VSR were 60% more likely to have gallstones compared to the lowest quartile (OR 1.596; 95% CI 1.074–2.373; p = 0.021). The study emphasizes that not only overall obesity, but also the distribution of abdominal fat is important in the formation of gallstones. The VSR ratio may serve as a useful imaging biomarker to identify men at increased risk of this disease.