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Background It has been 11 years since newborn screening started in Zhejiang in 1999.The aim of this study was to analyze and summarize the status of newborn screening in Zhejiang from 1999 to 2009.Methods Blood samples were collected from the heels of newborns 72 hours after birth.We have conducted laboratory tests that the congenital hypothyroidism (CH) and circulating levels of thyroid-stimulating hormone (TSH) was detected.Blood phenylalanine (Phe) was detected for phenylketonuria (PKU).Dissociation-enhanced lanthanide fluorescent immunoassay (DELFIA) was used for detection.Results From 1999 to 2009,3875228 newborns were screened and 2309 cases were confirmed as CH and 155 cases were confirmed as PKU.The incidence of CH and PKU were 1:1678 and 1:25 001 respectively.Conclusion In 11 years,the Zhejiang newborn screening center screened more than 3.8 million newboms,and helped more than 2000 CH and PKU patients to obtain early treatment in order to prevent physical disability and mental retardation.