BMI is the preferred measure of adiposity in adolescents. Recent evidence suggests that in adults the relationship between BMI and adiposity can vary by age and race/ethnicity. We investigated the relationship between BMI and percent body fat (%BF) in a large multi-ethnic, nationally representative sample of US adolescents (National Health and Nutrition Examination Survey, NHANES, 1999-2004). BMI was calculated; %BF was derived from dual-energy X-ray absorptiometry data and compared to BMI among adolescents from three groups: non-Hispanic white (NHW), non-Hispanic black (NHB), and Mexican-American (MA). Fractional polynomials were used to model a new equation to estimate %BF from a given BMI. MA boys weighed significantly less than either NHW or NHB boys, while only NHB girls weighed significantly more than the other girls. Among the boys there were no differences in mean BMI, whereas %BF differed significantly between all three groups. For the girls, both BMI and %BF differed significantly the groups with MA girls having the highest %BF. The significant correlates for modeling %BF from BMI included gender, age, race/ethnicity, weight, [formula in text]: the final model explained 79% of the variance in %BF. NHB adolescents had significantly lower %BF for BMI and MA had higher than NHW. Our results indicate that BMI may not be an equivalent measure of %BF in a multi-ethnic population of US adolescents.