Newborn adiposity, a nutritional measure of the maternal–fetal intra-uterine environment, is representative of future metabolic health. An anthropometric model using weight, length and flank skinfold to estimate neonatal fat mass has been used in numerous epidemiological studies. Air displacement plethysmography (ADP), a non-invasive technology to measure body composition, is impractical for large epidemiological studies. The study objective was to determine the consistency of the original anthropometric fat mass estimation equation with ADP. Full-term neonates were studied at 12–72 h of life with weight, length, head circumference, flank skinfold thickness and ADP measurements. Statistical analyses evaluated three models to predict neonatal fat mass. Lin’s concordance correlation coefficient, mean prediction error and root mean squared error between the predicted and observed ADP fat mass values were used to evaluate the models, where ADP was considered the gold standard. A multi-ethnic cohort of 468 neonates were studied. Models (M) for predicting fat mass were developed using 349 neonates from site 1, then independently evaluated in 119 neonates from site 2. M0 was the original anthropometric model, M1 used the same variables as M0 but with updated parameters and M2 additionally included head circumference. In the independent validation cohort, Lin’s concordance correlation estimates demonstrated reasonable accuracy (model 0: 0·843, 1: 0·732, 2: 0·747). Mean prediction error and root mean squared error in the independent validation was much smaller for M0 compared with M1 and M2. The original anthropometric model to estimate neonatal fat mass is reasonable for predicting ADP, thus we advocate its continued use in epidemiological studies.