Obstructive sleep apnea (OSA) and obesity are closely associated, and both have been reported to increase the risk of coronary heart disease. There is limited information on whether OSA is associated with coronary artery calcification (CAC), and whether this association is independent of obesity. A cross-sectional study observed the association between OSA and CAC among 258 healthy men aged 40 to 49 years of age, randomly selected from a population-based cohort. All individuals underwent overnight polysomnography and electron beam computed tomography to measure their apnea-hypopnea index (AHI) and the degree of CAC. In multivariate linear regression models containing potential cardiovascular risk factors except body mass index (BMI), AHI was significantly associated with CAC (P <0.01), but this association became insignificant after adjusting for BMI. In the logistic regression model including AHI and other covariates, the multivariate odds ratios [OR] (95% confidence interval [CI]) of the presence of CAC were 4.1 (95% CI 1.9 - 9.2) for men with a BMI between 23.0 and 27.4 kg/m2, and 15.1 (95% CI 4.6 - 49.3) for those with a BMI of 27.5 kg/m2 or greater, as compared to those with a BMI less than 23.0 kg/m2. In our cross-sectional observation, obstructive sleep apnea was positively associated with the presence and severity of coronary artery calcification, but this association was mediated by obesity. After taking into account potential cardiovascular risk factors, obesity was solely associated with coronary artery calcification, independent of the presence of OSA.