The optimum means of defining obesity in children is unclear, creating variation in practice, and hindering obesity surveillance, prevention and treatment. This study aimed to review evidence on the use of body mass index (BMI) and waist circumference for diagnosis of high body fat content and adverse cardiometabolic risk factors in children and adolescents. A systematic literature review was carried out and evidence appraised using the Quality Assessment of Studies of Diagnostic Accuracy in Systematic Reviews method. Literature searching began following the last systematic review of this topic (end 2001) and collected evidence in MEDLINE and EMBASE in 0- to 18-year-olds that compared the accuracy of BMI vs. waist circumference and compared BMI interpreted relative to national reference data vs. BMI interpreted relative to Cole/International Obesity Task Force international reference data. Ten studies compared diagnostic accuracy of BMI vs. waist circumference: they reported no improved identification of adverse cardiometabolic risk profiles from waist circumference over that provided by high BMI. Eight studies compared BMI with national reference data vs. the international approach: 5/8 found significantly poorer accuracy (lower sensitivity) using BMI with the international approach; 3/8 found similar sensitivity; in 7/7 studies that compared specificity this was similar. In conclusion, the present review provides no compelling evidence for use of either high waist circumference or BMI interpreted using the International Obesity Task Force approach in preference to the use of national BMI percentiles for the identification of children and adolescents with excess fatness and adverse cardiometabolic risk profile.