OBJECTIVE AND DESIGN: We investigated the impact of the fatness-related FTO rs9939609 A-allele on cross-sectional and longitudinal measures of body mass index (BMI), height and lean body mass (LBM) in a unique cohort representing a broad range of BMI. SUBJECTS AND MEASUREMENTS: A random sample of all men attending the Danish draft boards during 1943-1977 plus all men with a BMI>or=31.0 kg/m(2) (assuring representation of the right end of the distribution) was taken. Anthropometric measures were available at up to eight points in time from birth to adulthood in 1629 genotyped men. The odds ratio (OR) for being a carrier of FTO rs9939609 according to (1) one unit alteration in z-scores for BMI, height and LBM at given ages and (2) longitudinal changes in BMI and height z-scores were assessed by logistic regression. RESULTS: Except at birth, the AA genotype was associated with increased BMI z-scores at all point during the monitored lifespan, starting at the age of 7 years. This effect remained stable until early adulthood, where further weight gain occurred. The AA genotype was also--mainly through the effect on fatness--associated with accelerated linear growth in childhood (age 7 years; OR, 1.36; 95% confidence interval (CI), 1.06-1.74) and increased LBM in adulthood (OR, 1.24; 95% CI, 1.14-1.35). CONCLUSION: Fatness induced by FTO rs9939609 in early childhood is sustained until early adulthood, where further weight gain may occur. FTO rs9939609 may, however, also be associated with linear growth and LBM mainly through the effect on fat mass.