BACKGROUND Although identification of obesity during childhood is strongly recommended for the prevention of adult disease, access to obesity screening for children is almost exclusively through physicians' office visits. We examined the feasibility and utility of conducting a school-based obesity and cardiovascular disease (CVD) risk factor screening program in a rural Appalachian population. METHODS Height, weight, blood pressure, total cholesterol (TC), and high-density lipoprotein (HDL) cholesterol were measured in 1338 fifth-grade children (631 boys and 707 girls) in 14 rural West Virginia counties in 2000-2001. RESULTS We found a high prevalence of overweight (17.5%) and obesity (27.0%). Compared with non-overweight children, obese children had greater risk of high TC (OR 2.4), low HDL cholesterol (OR 5.3), high systolic blood pressure (OR 3.3), and high diastolic blood pressure (OR 2.4) (all OR >1.0, P < 0.05). Only 63% of obese and 26% of overweight children were identified by their physician as having a weight above recommended values. CONCLUSIONS The high prevalence of obesity, the associated clustering of CVD risk factors, and the low obesity identification rate by physicians suggest that alternative approaches to obesity screening, such as universal school-based programs, may be warranted in high-risk communities.