The pathobiological impact of individual components of the metabolic syndrome (MS) on cardiac structural and functional parameters in women with isolated MS is not known. The objectives of this study were (1) to compare biochemical (prothrombotic, lipogenic, and inflammatory) and imaging (carotid intima-media thickening and basic cardiac structural measurements) markers in women with and without MS and (2) to examine if any of these markers associated or predicted cardiac structural differences between the 2 groups. This cross-sectional pilot study included 88 women with MS and 35 women without it. MS was defined according to the National Cholesterol Education Program Adult Treatment Panel III criteria. Patients with diagnosis of diabetes were excluded. Compared with healthy subjects, women with MS had higher levels of intercellular adhesion molecule, myeloperoxidase, C-reactive protein, plasminogen activator inhibitor-1, leptin, apolipoprotein-B, and lower levels of apolipoprotein-A1 (p <0.001 for all). They also had higher mean ventricular septum, posterior wall thickness, left ventricular (LV) mass, carotid intima-media thickness (p <0.001 for all), and left atrial diameter (p = 0.015). In multivariable regression models, waist circumference and systolic blood pressure (BP) were significant predictors of: ventricular septum (p = 0.005 and p = 0.001, respectively), posterior wall thickness (p = 0.008 and p = 0.040, respectively), and LV mass (p <0.001 and p = 0.013, respectively). Significant predictors for carotid intima-media thickness were systolic BP, glucose, and leptin (p <0.0001, p = 0.034, and p = 0.002, respectively). In conclusion, there are significant clinical, biochemical, and cardiovascular structural differences in women with isolated MS compared with those without. Waist circumference and systolic BP had the strongest association with cardiac structural differences in this group of women.