Objective To summarize and analyze the results of external quality assessment (EQA) of phenylalanine (Phe) and thyroid stimulating hormone (TSH) during 2003-2012 in China and then provide a benchmark for the neonatal screening testing. Methods Referring to Newborn Screening Quality Assurance Program of Centers for Disease Control And Prevention and GB/T 20470-2006:Requirements of external quality assessment for clinical laboratories.With 3 times one year,5 controls were distributed to the participated laboratories each time.Then the laboratories were asked to measure and report the results back in a specified time.With appropriate statistical analysis,the performance of each laboratory was evaluated. Results During 2003-2012,the percent of each method used for Phe was from 54.9% to 85.2% for Fluorescence Analysis,from 12.6% to 6.2% for Quantitative Enzymatic Method,and from 35.4% to 4.6% for Guthrie Test.The percent of each method used for TSH was from 44.8% to 70.7% for Time Resolved Fluoroimmunoassay(TRFIA),from 36.0% to 11.2% for Enzyme-Linked Immunosorbent Assay(ELISA),and from 17.5% to 13.0% for Fluorescent-Enzyme immunoassay(FEIA).The inter-laboratory coefficient of variation(CV) during the 10 years were 12.13%,17.15%,and 12.14%~12.97% for each method of Phe.And for TSH,the inter-laboratory CV were 14.14%,14.88%~27.20%,and 17.07%~34.98% for each method,respectively.The average acceptable rates of Phe and TSH were 95.3% and 89.4% for quantitative testing,97.8% and 98.0% for qualitative clinical judgment. Conclusion The CV of Fluorescence Analysis and TRFIA are less than others,thus the TRFIA is the first choice for TSH testing in China.The external quality assessment of Phe and TSH for newborn screening is helpful to discover the problem in this area and promote the national quality level.