Objective: To assess body protein and protein deposition in prepubertal children with phenylketonuria (PKU)., Design: Cross-sectional study with nested longitudinal cohort., Setting: A tertiary referral paediatric hospital., Subjects: 37 PKU patients (3.9-11.0 years) and 27 unselected healthy controls (4.0-11.5 years) of whom 29 PKU patients and 17 controls were followed longitudinally., Interventions: All had measurements of height, weight, body fat and total body nitrogen (TBN) by neutron capture analysis; PKU patients and their unaffected siblings (n = 16) also had measurements of four day weighed food record and plasma amino acids by HPLC., Results: The children with PKU compared with the controls were significantly shorter (height SD score -0.42 +/- 0.89 vs 0.17 +/- 0.94, respectively, P < 0.02) and had a lower TBN (575 +/- 200 vs 710 +/- 215g, respectively, P < 0.02). TBN in the controls was significantly correlated with lean body mass (LBM), weight, height and age (r = 0.97, 0.95, 0.95, 0.88, respectively, P < 0.001). The children with PKU had significantly lower TBN when predicted from LBM, weight and age (93%, 92%, 92% of predicted, respectively), but normal TBN predicted from height (102% of expected). The annual accretion of nitrogen was similar for the PKU and controls (86 +/- 45 and 77 +/- 58 g/y, respectively). There was no difference between the two groups in protein intake or plasma amino acids except for phenylalanine., Conclusion: The children with PKU had a deficit in height and body protein despite a normal to higher accretion of protein. If the deficit occurs early in life, amino acid supplementation and other nutritional practices used at this time need to be reviewed.