Objective To analyze the screening result of neonatal hereditary metabolic disease from January 2007 to December 2013 in Xiamen and Longyan city and to explore the incidence rates and diagnostic status of congenital hypothyroidism( CH) and phenylketonuria( PKU) in 638 171 neonates. Methods Blood specimen were collected from heel of neonates delivered within 72 hours.The concentrations of thyroid stimulating hormone( TSH) and phenlalanine( Phe) were measured by time-resolved fluorescence immunoassay( Tr-FIA) and fluorometric. Neonates with positive CH or PKU and borderline case were followed up in order to observe their intelligence developments. Results The incidence rates of PKU and CH in 638 171 neonates were 1 /39 886 and 1 /1 078 respectively,and the cure rates in neonates with PKU and CH were 96. 65% and 98. 31% respectively. Twenty three neonates had different degrees of intelligence development disorders. Conclusion Screening for neonatal diseases is a key point in early detection and treatment of CH and PKU. Early prevention and treatment can avoid or reduce the disorders of intelligence and psychological developments.