Cardiovascular disease (CVD) is a major cause of death in the female population. The current study aimed to examine the relationship between CVD risk and novel endothelial dysfunction biomarkers [i.e., endocan, adiponectin and intercellular adhesion molecule (ICAM)-1] and carotid intima-media thickness (cIMT), respectively in a cohort of disease-free women of reproductive age. A total of 129 women were selected. Serum endocan, adiponectin and ICAM-1 were measured by a commercial enzyme-linked immunosorbent assay and cITM was determined by ultrasound. Cardiovascular risk score (CVRS) was calculated. The lowest endocan (p for trend = 0.051) and adiponectin (p for trend = 0.040) levels were found in a group of subjects with the highest CVRS. The cIMT values were the highest in second tertile subgroups, with the highest 75th percentile in a third tertile CVRS group, while the lowest cIMT values were detected in the lowest CVRS tertile group (p for trend = 0.001). A significant positive correlation between cIMT and CVRS (ρ = 0.307, p < 0.001), and a negative correlation between adiponectin and endocan with CVRS, respectively (ρ = - 0.252, p = 0.004; ρ = - 0.179, p = 0.043) were observed, but only endocan retained the independent association with CVRS (p = 0.030) in the multiple linear regression analysis. Endocan could be useful diagnostic tool in the estimation of cardiovascular risk in young women.