Introduction: Cardiovascular disease (CVD) and its risk factors show clear socioeconomic gradients in Canadian adults. Whether socioeconomic gradients in cardiovascular risk emerge in childhood remains unclear. The objective of this study was to determine whether there are socioeconomic gradients in physiological markers of CVD risk in Canadian children and adolescents. Methods: Using combined cross-sectional data from the Canadian Health Measures Survey 2007–2011, we examined the following cardiovascular risk markers: overweight (including obesity), aerobic fitness score (AFS), blood pressure (BP), blood lipids (total as well as HDL and LDL cholesterol and triglycerides), glucose metabolism and C-reactive protein (CRP) by sex in 2149 children (ages 6–11 years) and 2073 adolescents (ages 12–17 years). Multivariate linear and logistic regression analyses were used to identify patterns in cardiovascular risk across strata of household income adequacy and parental educational attainment, adjusting for age and ethnicity, and stratified by age group and sex. Results: Young boys showed markedly higher prevalence of obesity than young girls (prevalence of 18.5%, 95% confidence interval [CI]: 15.6–21.5 vs. 7.7%, 95% CI: 5.2–10.3). However, negative SES gradients in adiposity risk were seen in young and adolescent girls rather than boys. Young and adolescent boys were more physically fit than girls (mean AFS of 541, 95% CI: 534–546 vs. 501, 95% CI: 498–505 in children; 522, 95% CI: 514–529 vs. 460, 95% CI: 454–466 in adolescents; p < .001). Although a positive income gradient in AFS was observed in both boys and girls, statistical significance was reached only in girls (p = .006). A negative gradient of parental education in BP was observed in young children. While we observed substantial sex differences in systolic BP, total and HDL cholesterol, fasting glucose and CRP in adolescents, sex-specific socioeconomic gradients were only observed for systolic BP, HDL and LDL cholesterol. Further studies with large samples are needed to confirm these findings. Conclusion : This study identified important sex difference and socioeconomic gradients in adiposity, aerobic fitness and physiological markers of CVD risk in Canadian school-aged children. Population health interventions to reduce socioeconomic gradients in CVD risk should start in childhood, with a particular focus on preventing obesity in young boys of all SES and girls of low SES, promoting physical fitness especially in girls and in all ages of youth in low-SES groups, and increasing parental awareness, especially those with low educational attainment, of early CVD risks in their children.