Since December 2001, a total of 52 obese schoolchildren and 38 non-obese controls have undergone vascular ultrasound at our institution. From this cohort, we enrolled 40 obese children (16 girls, median age 12 years, mean body mass index (BMI) 27.5±4.6 kg/m2) and 26 non-obese peers (12 girls, median age 12 years, mean BMI 16.1±2.4 kg/m2) for the present study. We analysed the association between obesity, subclinical atherosclerosis and haemorheological variables, including whole blood viscosity (WBV) at four different shear rates (200 s-1, 30 s-1, 5 s-1 and 1 s-1), plasma viscosity, and serum lipid concentrations. Blood lipids and apolipoproteins were also determined and correlated with carotid intima-media thickness (IMT) and flow-mediated dilatation (FMD) of the brachial artery, measured by high-resolution ultrasonography. WBV at 200 s-1, 30 s-1 and 5 s-1, as well as plasma viscosity, were significantly higher in the obesity group (all P <0.01). No difference was seen for WBV at 1 s-1, erythrocyte aggregation and haematocrit. WBV at high shear rates was significantly associated with BMI, increased IMT and decreased FMD ( P <0.05). After controlling for BMI on stepwise linear regression, WBV at 30 s-1 was the strongest predictor of IMT ( P <0.01) and FMD ( P <0.05) among our study variables. Conclusion: Hyperviscosity is related to subclinical atherosclerosis in obese schoolchildren. Viscosity parameters contribute new information in addition to body mass index, blood pressure and blood lipids and may help to facilitate risk stratification in obese paediatric patients.