Background: Both obstructive sleep apnea syndrome (OSAS) and coronary artery calcification (CAC) are considered to be related with the presence of coronary artery disease (CAD). In this study we evaluate the association between OSAS and presence of subclinical atherosclerosis assessed by tomographic coronary calcium score in patients who had OSAS but no history of known CAD. Methods: Seventy-three patients who were asymptomatic for CAD and had suspected OSAS were referred to overnight attended polysomnography. Patients were classified into 4 groups according to the Apnea-Hypopnea Index (AHI). All patients underwent computed tomographic examination for tomographic coronary calcification scoring. Physical examination, sleep study recordings, complete blood count and serum biochemistry were obtained from all patients. Results: In the whole group, AHI levels were weakly correlated with coronary calcium score (r = 0.342, p = 0.003) and body mass index (r = 0.337, p = 0.004), moderately correlated with basal oxygen saturation (r = −0.734, p < 0.001), and strongly correlated with oxygen desaturation index (r = 0.844, p < 0.001). In an univariate analysis, age, AHI, basal oxygen saturation, and oxygen desaturation index were associated with CAC in patients with OSAS. In a multiple logistic regression model, age (OR 1.108,%95 CI 1.031-1.191, p = 0.005) and AHI (OR 1.036,% 95 CI 1.003-1.070, p = 0.033) were only independent predictors of CAC in patients with OSAS with a sensitivity of 88.9% and 77.8% and a specificity of 54.3% and 56.5% respectively. Conclusions: Our findings suggest that in patients with moderate or severe OSAS and advanced age, physicians should be alert for the presence of subclinical atherosclerosis.