This study assessed markers of vascular endothelial cell dysfunction associated with early atherosclerosis in carotid arteries. We measured the plasma levels of free-form tissue factor pathway inhibitor (free TFPI), plasminogen activator inhibitor-1 (PAI-1), and von Willebrand factor (vWF) in 522 adults without cardiovascular disease enrolled in the Suita Study. For each sex, we analyzed the association of the degree of intimal-medial thickness (IMT) with hemostatic markers using logistic regression analysis considering potential confounding risk factors, including age, body mass index, lifestyle (current smoking and drinking), illness (diabetes mellitus and hyperlipidemia), systolic blood pressure, and antihypertensive drug use. The age-adjusted levels of free TFPI and PAI-1 were positively and independently associated with the degree of IMT for men. Even after adjustment for all confounding factors, the level of PAI-1 was positively associated with the degree of IMT. These results indicate that measurement of the levels of free TFPI and PAI-1 is a potentially useful tool for the detection of early atherosclerosis in men.