In adults, overweight is often associated with other cardiovascular disease (CVD) risk factors. We determined whether these associations were also present in young children. This study examined the relationships between elevated BMI (≥85th and ≥95th percentiles for age and sex) and the highest quintile of waist circumference (WC) with CVD risk factors, including fasting triglyceride (TGL), high- and low-density lipoprotein (HDL and LDL), total cholesterol (TC), non-HDL cholesterol, and C-reactive protein (CRP) in 3,644 3- to 6-year-old children included in the 1999–2008 National Health and Nutrition Examination Surveys (NHANES). Results showed that 20% (highest quintile) of the sample had a TC >170 mg/dl, LDL >109 mg/dl, TGL >103 mg/dl, non-HDL >128 mg/dl, CRP >0.13 mg/dl, WC >57.2 cm, and HDL <42 mg/dl. Increased BMI and WC were associated with increased CRP levels in non-Hispanic black boys and girls, Hispanic boys, and non-Hispanic white girls, whereas elevated TGL and non-HDL cholesterol and low HDL cholesterol were generally associated with elevated BMI and WC in Hispanic children. TC and LDL cholesterol were not significantly associated with elevated weight in 3- to 6-year-olds. BMI and WC were similar in predicting the same risk factors. In summary, this analysis shows that in preschool-age children, greater BMI and WC are associated with biomarkers that are related to CVD risk, but these associations vary by ethnicity. Child health providers should consider using both BMI and WC to identify young children who may be at risk for elevated CVD biomarkers.