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To assess sex-specific differences regarding use of conventional risks and coronary artery calcification (CAC) to detect coronary artery disease (CAD) using coronary CT angiography (CCTA).The Nationwide Gender-specific Atherosclerosis Determinants Estimation and Ischemic Cardiovascular Disease Prospective Cohort study is a prospective, multicentre, nationwide cohort study. Candidates with suspected CAD aged 50–74 years enrolled from 2008 to 2012. The outcome was obstructive CAD defined as any stenosis ≥50% by CCTA. We constructed logistic regression models for obstructive CAD adjusted for conventional risks (clinical model) and CAC score. Improvement in discrimination beyond risks was assessed by C-statistic; net reclassification index (NRI) for CAD probability of low (<30%), intermediate (30%–60%) and high (≥60%); and risk stratification capacity.Among 991 patients (456 women, 535 men; 65.2 vs 64.4 years old), women had lower CAC scores (median, 4 vs 60) and lower CAD prevalence (21.7% vs 37.0%) than men. CAC significantly improved model discrimination compared with clinical model in both sexes (0.66–0.79 in women vs 0.61–0.83 in men). The NRI for women was 0.33, which was much lower than that for men (0.71). Adding CAC to clinical model had a larger benefit in terms of moving an additional 43.3% of men to the most determinant categories (high or low risk) compared with −1.4% of women.The addition of CAC to a prediction model based on conventional variables significantly improved the classification of risk in suspected patients with CAD, with sex differences influencing the predictive ability.UMIN-CTR Clinical Trial: UMIN000001577.