Phenylketonuria (PKU) is one of the commonest inborn error of metabolism, it is an autosomal recessive metabolic genetic disorder characterized by a mutation in the gene for the hepatic enzyme phenylalanine hydroxylase (PAH), rendering it nonfunctional. The diagnosis of this disorder can be confirmed by analysis of urine components. The present study aimed to assess the prevalence of PKU among children aged 6 months to 6 years in Sohag governorate Egypt, its relationship to malnutrition and identifying families with higher predisposition to having children with inborn errors of metabolism. One hundred children were selected from 18,000 patients seen in the pediatric neuropsychiatry clinic of Sohag University hospital over three years, between May 2008 - May 2011. They were presented with clinical symptoms suggestive of probable preliminary diagnosis of PKU. Proper clinical and laboratory investigations, including ferric chloride test in urine, total protein and albumin in serum, were screened to confirm the diagnosis. PKU was diagnosed in two children cases. The diagnosed cases were suffering from mild malnutrition represented by low levels of serum albumin and total protein comparable to cases of Marasmus and kwashiorkor or other deficiencies like rickets. Screening of the newborn with  special emphasis on PKU is highly recommended before discharge from the nursery for children delivered in the hospital or on first visit to the clinic for children delivered at home. Early detection would help prevent serious and permanent neurological impairment.