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Background: Skinfold thickness (SFT) measurements are a reliable and feasible method for assessing body fat in children but their use and interpretation is hindered by the scarcity of reference values in representative populations of children. The objectives of the present study were to develop age- and sex-specific percentile curves for five SFT measures (biceps, triceps, subscapular, suprailiac, medial calf) and to describe body fat composition in a representative population of Canadian children and youth. Methods: We analyzed data from 3938 children and adolescents between 6 and 19 years of age who participated in the Canadian Health Measures Survey cycles 1 (2007/2009) and 2 (2009/2011). Standardized procedures were used to measure SFT. Age- and sex-specific centiles for skinfolds and body fat were calculated using the GAMLSS method. Results: Percentile curves were materially different in absolute value and shape for boys and girls. Percentile girls in girls steadily increased with age whereas percentile curves in boys were characterized by a pubertal centered peak. Median body fat percentage at age 18 was 13.2 and 25.4% among boys and girls, respectively. Conclusions: The current study has presented for the first time percentile curves for five SFT measures and body fat in a representative sample of Canadian children and youth.