Objective The ratio of apolipoprotein B (apoB) and apolipoprotein A1 (apoA1) has been associated with significant coronary stenosis detected by conventional coronary angiography. However, the optimal apoB/A1 cut-off for identifying subjects with significant coronary stenosis, especially using coronary multidetector computed tomography (MDCT), has not been determined. We therefore investigated whether apoB/A1 ratio could predict occult coronary atherosclerosis detected by coronary MDCT and we determined the optimal cut-off value of apoB/A1 ratio in detecting subjects with occult coronary atherosclerosis. Methods This cross-sectional study included 1,401 subjects (877 men and 524 women) who underwent coronary MDCT and measurements of serum apoB and apoA1 during routine health screening examinations at the Asan Medical Center, Seoul, Republic of Korea. Results Significant coronary artery stenosis was detected in 114 subjects (8.1%), 89 men and 25 women. An increase in apoB/A1 quartiles was associated with increased percentages of subjects with significant coronary stenosis and noncalcified plaques (NCAP). After adjustment for confounding variables, each 0.1 increase in serum apoB/A1 was significantly associated with increased odds ratios [ORs] for coronary stenosis and NCAP of 1.23 (95% confidence interval [CI], 1.11-1.36) and 1.19 (95% CI, 1.10-1.29), respectively. The optimal apoB/A1 ratio cut off value for MDCT detection of significant coronary stenosis was 0.58, which had a sensitivity of 70.2% and a specificity of 48.2% (area under the curve=0.61, 95% CI=0.58-0.63, P＜0.001). Conclusion Our results indicate that apoB/A1 ratio is a good indicator of occult coronary atherosclerosis detected by coronary MDCT and that subjects with apoB/A1 ratio greater than 0.58 are good candidates for coronary MDCT.