Background Obesity is a world-wide epidemic whose prevalence is underestimated by BMI measurements, but CUN-BAE (Clínica Universidad de Navarra - Body Adiposity Estimator) estimates the percentage of body fat (BF) while incorporating information on sex and age, thus giving a better match. Our aim is to compare the BMI and CUN-BAE in determining the population attributable fraction (AFp) for obesity as a cause of chronic diseases. Methods We calculated the Pearson correlation coefficient between BMI and CUN-BAE, the Kappa index and the internal validity of the BMI. The risks of arterial hypertension (AHT) and diabetes mellitus (DM) and the AFp for obesity were assessed using both the BMI and CUN-BAE. Results 3888 white subjects were investigated. The overall correlation between BMI and CUN-BAE was R2 = 0.48, which improved when sex and age were taken into account (R2 > 0.90). The Kappa coefficient for diagnosis of obesity was low (28.7 %). The AFp was 50 % higher for DM and double for AHT when CUN-BAE was used. Conclusions The overall correlation between BMI and CUN-BAE was not good. The AFp of obesity for AHT and DM may be underestimated if assessed using the BMI, as may the prevalence of obesity when estimated from the percentage of BF.