Background: Phenylketonuria is a hereditary, autosomal recessive disorder caused by deficiency of phenylalanine hydroxylase or its cofactor tetrahydrobiopterin. The purpose of the present study was to evaluate the incidence of this disorder in southern Iran. Methods: All the neonates born between 22/Dec/2004 and 7/Sep/2007 were screened and their blood samples were tested by colorimetric and high performance liquid chromatography methods to obtain a diagnosis of phenylketonuria. Results: Of the screened newborns (87091 females and 88143 males) 15 female and 13 male neonates were diagnosed definitely as having phenylketonuria. Conclusion: The incidence of phenylketonuria in girls and boys was 1.7 in 10000 and 1.5 in 10000, respectively (mean: 1.6 in 10000) in southern Iran (Fars province).