Adrenarche is characterized by steadily rising levels of adrenal androgen metabolites from 4–6 years of age. We recently described marked gender-specific differences in circulating ratios between selected adrenal androgen metabolites in a cross-sectional study. This may suggest gender differences in steroidogenic enzyme activities. We therefore aimed at verifying these findings in a prospective, longitudinal study of healthy boys and girls who were examined during pubertal transition.A longitudinal study of 20 healthy children from the COPENHAGEN Puberty Study, followed every 6 months for 5 years. Clinical examinations were conducted and serum concentrations of Androstenedione (Adione), 17-hydroxyprogesterone (17-OHP), testosterone (T), dehydroepiandrosterone (DHEA) and DHEA sulfate (DHEAS) were quantified by a newly developed LC-MS/MS method. DHEA, DHEAS, Adione, 17-OHP and T increase with age. Boys had higher levels of DHEAS from 10.5 years of age, whereas girls had higher levels of Adione from 13 years of age compared to boys. Interestingly, we observed significantly higher ratios of DHEAS/DHEA (sulfotransferase activity) in boys before and after pubertal onset compared to girls, whereas Adione/17-OHP (CYP 17 activity) appeared to increase more in pubertal girls compared to boys. This suggests that adrenal steroidogenic enzyme activities show developmental as well as gender-specific changes in healthy children.