The aim of the study was to assess body composition in subjects with phenylketonuria (PKU). Forty-five patients aged 13.8 ± 5.2 years were evaluated. Among them, 15 patients had not reached sexual maturity, showing normal serum values of phenylalanine (Phe) (subgroup 1), and 30 subjects were sexually mature (Tanner 5 stage), showing either normal serum Phe (18 cases; subgroup 2a) or increased serum Phe (12 cases; subgroup 2b). DXA-assessed spine and total body (TB) measurements [bone mineral density (BMD), bone mineral content (BMC), lean body mass (LBM) and the calculated ratios BMC/LBM] as well as laboratory parameters (serum carboxyterminal telopeptide of type I collagen, bone alkaline phosphatase, osteocalcin, parathormone, calcitonin, total and ionized calcium) were analyzed. Statistically significant differences were revealed between subgroup 1 versus 2a for TB BMC/LBM ratio SD scores and between subgroup 2a versus 2b for TB BMD, spine BMD, TB BMC/LBM ratio and spine BMC/LBM ratio SD scores. Stepwise multiple regression analysis revealed that serum Phe negatively affected bone status. The skeletal status in children with PKU is impaired by the disease. Applying body composition parameters instead of BMD alone may reflect the level of impairment in a new, different way.