Objective To carry out the current status of internal quality control by statistical analysis of the Internal Quality Control(IQC) data of neonatal screening in 2011, which including phenylalanine (Phe) and thyrotropin-stimulating hormone (TSH). Methods After collecting the internal quality control information and data (raw data, manufacturers information, control rules, lots, numbers of results, coefficient variations of data under control, coefficient of variations of cumulative data under control, methods, instrument manufacturers and models, reagents) of Phe and TSH testing from the external quality control software, coefficient variations of every month and long time duration of Phe and TSH internal quality control had been calculated and analyzed, then comparing with the one third and one forth of acceptable total error (10% and 7.5%) in order to evaluate whether could satisfy the provided quality requirements. Results The return rates of IQC Results ranged from 61.78% to 91.62% of 12 months in 2011, 84.86% for average.There were 80 (49%) laboratories select 1_2S or 1_3S for quality control rules while the remaining (51%) use Westgard multi-rules.The totally rates of CVs of Phe and TSH (2 lots) less than 1/3 TEa were 54.63% and 64.54% (Phe), 58.25% and 62.35% (TSH) respectively; less than 1/4 TEa were 29.14% and 34.48% (Phe), 27.70% and 28.08% (TSH) respectively; for cumulative data the CVs less than 1/3 TEa were 53.20% and 59.12% (Phe), 57.47% and 56.21% (TSH) respectively; less than 1/4 TEa were 26.46% and 28.12% (Phe), 25.64% and 25.87% (TSH) respectively.The most laboratories did not reach the acceptable imprecision level and most of them should improve their precision performances. Conclusion The testing capabilities and performances of neonatal screening laboratories of Phe and TSH can be objectively evaluated by the quality specifications of acceptable imprecision (less than 1/3 TEa or 1/4 TEa) and more work should be done to improve the testing quality of neonatal laboratories in China.