BACKGROUND Phenylketonuria (PKU) treatment consists of life-long protein restriction and Phe-free medical foods for adequate nutritional intake and growth. A relationship between body composition and blood phenylalanine (Phe) concentrations in subjects with PKU has been proposed but this has not been consistently reported. METHODS Dietary intake, lean body mass (LBM) and fat mass (FM) were measured in 30 pediatric subjects with PKU compared to 30 age, and sex matched controls. The relationship between body composition and blood Phe was analyzed within the PKU cohort from clinically collected dried blood spot Phe concentrations. RESULTS Male subjects with PKU had less LBM% and more FM% than controls (p = .024). There was no difference in LBM% and FM% among female subjects. Age (p = .02) and FM% (p = .02) were positively correlated to dried blood spot Phe. Synthetic protein intake (g/kg body weight) was negatively correlated with dried blood spot Phe (p = .04). Natural protein intake was not related to blood spot Phe. CONCLUSIONS Children with PKU face additional dietary challenges maintaining healthy growth and body composition while keeping Phe levels low. We observed higher FM% and lower LBM% in male subjects with PKU. Correlations do not prove cause and effect but suggest a relationship between increased blood Phe, lower synthetic protein intake and increased FM%. Future studies may explore if lower blood Phe concentrations is associated with a lower FM% and higher LBM%; particularly among adult patients now managed on pegvaliase (Palynziq®) who consume normal amounts of natural protein or among younger patients who consume glycomacropeptide (GMP).