Cardiovascular disease (CVD) originates in childhood and early identification of risk factors provides an early intervention opportunity. The aim was to identify children at higher risk using a CVD risk score, developed from factors known to cluster in childhood. Risk was scored as very high (≥97.5th centile), high (≥95th), moderate (≥90th) or threshold (<90th) using normal pediatric reference ranges for 10 common biomedical risk factors. These were summed in a multifactor CVD risk score and applied to a sample of 285 observations from 136 overweight Australian children (41% male, aged 7–12 years). Strength of associations between CVD risk score and individual biomedical and dietary variables were assessed using univariate logistic regression. High waist circumference (Odds Ratio: 5.48 [95% CI: 2.60–11.55]), body mass index (OR: 3.22 [1.98–5.26]), serum insulin (OR: 3.37 [2.56–4.42]) and triglycerides (OR: 3.02 [2.22–4.12]) were all significantly related to CVD risk score. High intakes of total fat (OR: 4.44 [1.19–16.60]), sugar (OR: 2.82 [1.54–5.15]) and carbohydrate (OR 1.75 [1.11–2.77]) were significantly related to CVD risk score in boys only. This multifactor CVD risk score could be a useful tool for researchers to identify elevated risk in children. Further research is warranted to examine sex-specific dietary factors related to CVD risk in children.