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To describe the prevalence of obesity as estimated by waist circumference (WC) and body mass index (BMI) and compare associations of WC and BMI with indicators of metabolic, cardiovascular, and renal health in children with chronic kidney disease (CKD).Cross-sectional analysis stratified by CKD etiology (nonglomerular or glomerular) of 737 subjects. The kappa statistic was used to assess agreement between the 2 measures of obesity. Linear regression models were performed using WC and BMI as separate independent variables. Dependent variables included lipid measures, insulin resistance, blood pressure, left ventricular mass index, proteinuria, and estimated glomerular filtration rate. Associations were scaled to SD and interpreted as the change in dependent variable associated with a 1-SD change in WC or BMI.There was good agreement (kappa statistic = 0.68) between WC and BMI in identifying obesity. Approximately 10% of subjects had obesity by 1 measure but not the other. BMI was more strongly associated with estimated glomerular filtration rate than WC. BMI was more strongly associated with left ventricular mass index in the nonglomerular CKD group compared with WC, but both had significant associations. The associations between WC and BMI with the remainder of the dependent variables were not significantly different.Measurement of WC added limited information to BMI in this cohort. Further longitudinal study is needed to determine how WC and BMI compare in predicting outcomes, particularly for children with CKD identified as having obesity by 1 measure but not the other.