Objetive To analyze the results of neonatal phenylketonuria(PKU) and congenital hypothyroidism(CH) screening of Sichuan province from 2000 to 2009 and provide scientific basis for health bureau to make decision. Methods The medical staff of blood collection units carried out health education of neonatal screening,collected,saved and delivered the newborn blood samples after parents informed consent;The medical staff of the neonatal screening center accepted the blood samples timely,detected the qualified samples for screening of PKU and CH,reviewed the suspicious or positive results,noticed the confirmed positive results. Results The neonatal screening rate and coverage rate were increased significantly year by year in Sichuan province from 2000 to 2009,the neonatal screening rate reached 67.50%,the coverage rate of city (state) reached 100%,the coverage rate of county (district) reached 87.29%,the coverage rate of blood collection units reached 90.98% in 2009;In total there were 1 721 340 newborns screened from 2000 to 2009,67 cases of PKU were identified with a detectable rate of 1∶25 692,699 cases of CH were identified with a detectable rate of 1∶2 573. Conclusions The work of neonatal PKU and CH screening in Sichuan province has achieved significant results in the past 10 years,it has showed obvious social benefits.The current rate of neonatal screening have room to improve further,screening work remained to be in-depth further.