There is increasing evidence that cortisol contributes to cardiovascular risk. It is unclear whether physiological concentrations of serum cortisol are related to vascular risk markers in children. The cross-sectional associations between morning serum cortisol and cardiovascular risk markers: blood pressure (BP) and carotid intima-media thickness (IMT), were examined in a sample of healthy prepubertal children (age, 6.8 ± 0.1 y) attending primary care clinics. Serum cortisol was associated with increased systolic BP (SBP; n = 223; p < 0.001) and carotid IMT (n = 91; p < 0.0001). These associations were independent from age, BMI, body fat, waist, insulin resistance, serum lipids, and heart rate (HR). No gender interactions were apparent in these associations. In summary, a higher morning serum cortisol within the physiological range is in prepubertal children associated with vascular risk markers. Because childhood risk factors predict adult risk for cardiovascular disease, these observations may have implications in the prevention of cardiovascular disease early in life.