P>Objective The number of CAG repeats within the CAG repeat polymorphism of the androgen receptor (AR) gene correlates inversely with the transactivation of the receptor. We investigated the relationship between the AR CAG repeat polymorphism and longitudinal growth, puberty and body composition from prepuberty until young adult age. Design Observational study with repeated measurements. Subjects Two comparable young Dutch cohorts. The first cohort consisted of 226 subjects. Measurements were performed from 13 until 36 years of age. The second cohort consisted of 244 subjects. Measurements in this cohort were performed from 8 until 14 years of age. Measurements Associations between height, height velocity, weight, BMI, fat mass, fat-free mass and pubertal development and CAG repeat length were measured. Results Height-standard deviation scores (SDS) were inversely associated with AR CAG repeat length in boys at young, prepubertal and early pubertal age. This association diminishes in the following years and completely disappears after the age of 16 years. No associations were found with pubertal stage or any of the other parameters for body composition. Conclusions AR CAG repeat length is inversely associated with longitudinal height in young boys, before the onset of puberty. During puberty, these differences disappear, possibly overruled by a strongly developing hypothalamic-pituitary-gonadal axis.