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Research suggests that there has been a leveling off in obesity prevalence occurring in the child population. However, a concern with the evidence base is that all of the studies have relied upon the use of BMI. The purpose of this study was to compare waist circumference (WC), BMI, and waist-to-height ratio (WHtR) data in three different sample of children (total number: 14,697) typically aged 11–12 years. Obesity prevalence defined by BMI did not change significantly between measurement years (2005 boys 20.6%, girls 18.0%; 2006 boys 19.3%, girls 17.3%; 2007 boys 19.8%, girls 16.4%). Obesity prevalence defined by WC was considerably higher especially, in girls (2005 boys 26.3%, girls 35.6%; 2006 boys 20.3%, girls 28.2%; 2007 boys 22.1%, girls 30.1%). The prevalence of children defined as “at risk” according to WHtR (2005 boys 23.3%, girls 21.1%; 2006 boys 16.7%, girls 15.6%; 2007 boys 17.6%, girls 17.2%) was found to be between obesity prevalence, estimated using BMI and WC. This data are the most up to date collection that includes BMI and WC in three large samples of children and clearly demonstrates inconsistencies between different measurements based on current classification systems. There is a need to understand the relationship between BMI and WC, with growth and health risk to establish a consistent public health message that is easily understood by the public.