Abstract Background The clinical presentation of ischemic heart disease in women differs from men, which could reflect sex-related differences of normal physiology. Cardiac CT angiography provides a noninvasive method to assess both regional and transmural myocardial perfusion in addition to coronary atherosclerosis. Objective The aim of this study was to evaluate potential sex-related differences of (1) left ventricular (LV) myocardial perfusion measured as LV myocardial attenuation density/LV blood pool attenuation density (MyoAD -ratio) at rest and (2) transmural perfusion ratio (TPR) as a measure of endocardial perfusion relative to epicardial perfusion. Methods Myocardial perfusion at rest and coronary artery atherosclerosis were evaluated with multidetector CT in 206 asymptomatic women and 203 age-matched men from the Copenhagen General Population Study. Results LV myocardial perfusion at rest (LV MyoAD -ratio) was higher in women than in men (9% difference; P  = 0.039). In a multivariable analysis, including age, sex, cardiovascular risk factors, Agatston score, and presence of coronary stenosis, global LV MyoAD -ratio remained significantly higher in women than in men ( P  = 0.045). No effect of cardiovascular risk factors on myocardial perfusion at rest was noted. Myocardial perfusion at rest was correlated to age in men ( r  = 0.15, P  = 0.031) but not in women ( r  = −0.01, P  = 0.83). TPR was slightly lower in women than in men (1.12 vs 1.14; P  = 0.0019). Conclusion LV myocardial perfusion at rest is higher in women than men independent of coronary atherosclerosis in asymptomatic subjects with risk factors.