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Factor VII-activating protease (FSAP) may regulate development of cardiovascular disease (CVD). We evaluated sex differences in FSAP measures and examined the association between FSAP and coronary artery calcification (CAC) in a middle-aged population. Participants were randomly selected citizens aged 50 or 60 without CVD, diabetes mellitus, Marburg I polymorphism, or hormone replacement therapy (HRT). FSAP protein concentration (total FSAP), FSAP urokinase-activating capacity (FSAP GP), and FSAP GP/total FSAP (specific FSAP activity) were measured. Cardiac computed tomography (CT) determined the Agatston score, dividing the study population in three groups: (1) Agatston score = 0 U, (2) Agatston score = 1–99 U, or (3) Agatston score more than 99 U. A total of 134 women and 116 men were included. Total FSAP, FSAP GP, and specific FSAP activity were independently higher in women (97.4%, 81.1%, 0.84, respectively) compared with men (87.5%, 68.7%, 0.79, respectively) (P < 0.001). In women, total FSAP was significantly different between (3) Agatston score (111.5%) and (1) Agatston score (95.4%), respectively, (2) Agatston score (96.8%), (P < 0.05). Also, the specific activity of FSAP was significantly different between (3) Agatston score (0.77) and (1) Agatston score (0.85), respectively, (2) Agatston score (0.86) (P < 0.05). No difference in FSAP measures was observed in men. FSAP measures are higher in women compared with age-matched men. The extent of CAC in women is positively associated with total FSAP, but negatively associated with the specific activity of FSAP suggesting that FSAP may play a role in the evolution of CVD in women.