Waist circumference (WC) and waist-to-height ratio (WHtR) are often used as indices predictive of central obesity. The aims of this study were: 1) to obtain smoothed centile charts and LMS tables for WC and WHtR among Colombian children and adolescents; 2) to evaluate the utility of these parameters as predictors of overweight and obesity. A cross-sectional study was conducted of a sample population of 7954 healthy Colombian schoolchildren [3460 boys and 4494 girls, mean age 12.8 (±2.3) years]. Weight, height, body mass index (BMI), WC and WHtR were measured, and percentiles were calculated using the LMS method (Box-Cox, median and coefficient of variation). Appropriate cut-off points of WC and WHtR for overweight and obesity, according to International Obesity Task Force definitions, were selected using receiver operating characteristic (ROC) analysis. The discriminating power of WC and WHtR is expressed as area under the curve (AUC). Reference values for WC and WHtR are presented. Mean WC increased and WHtR decreased with age for both genders. A moderate positive correlation was observed between WC and BMI (r = 0.756, P < 0.01) and between WHtR and BMI (r = 0.604, P < 0.01). ROC analysis revealed strong discrimination power in the identification of overweight and obesity for both measures in our sample population. Overall, WHtR was a slightly better predictor of overweight/obesity (AUC 95% CI 0.868–0.916) than WC (AUC 95% CI 0.862–0.904). This paper presents the first sex and age-specific WC and WHtR percentiles for Colombian children and adolescents aged 9.0–17.9 years. The LMS tables obtained, based on Colombian reference data, can be used as quantitative tools for the study of obesity and its comorbidities.