Body fat assessment in children and adolescents is an important indicator of nutritional status. Prediction equations are widely used for the estimation of body fatness in clinical setting. To date, there are no reported studies that examined the validity of skinfold equations in predicting body fat among children in Malaysia. Hence, this study aimed to investigate the predictive validity of previously published skinfold equations in estimating body fat percentage (%BF) of Malaysian children. A total of 370 healthy Malay children (185 boys; 185 girls) aged 9-14 years participated in this study. Height, weight, skinfold at five sites (triceps, biceps, subscapular, iliac crest and medial calf) were measured. Deuterium dilution (D2O) technique was used as criterion method for estimation of total body water and fat-free-mass (FFM). Fat-mass was derived from the difference between weight and FFM, and %BF was then calculated. Among all skinfold equations, Bland-Altman analysis showed Lohman’s and Liu’s equations had closer absolute values with the least bias and small limits of agreement against D2O (boys: -4.3 to 1.7%; girls:-1.4 to -6.0%; ICC: 0.6-0.7). Slaughter’s and Deurenberg’s equations underestimated %BF with large bias and large limits of agreement (boys: -8.3 to -13.8%; girls: -11.0 to -16.3%; ICC: 0.4-0.6). In conclusion, previously published skinfold equations underestimated %BF of Malaysian children. Thus, we opine that population-specific skinfold prediction equations that can accurately estimate body fatness of Malaysian children needs to be developed for application in the clinical setting as well as in future studies.