Abstract: Objective：To analyze and discuss the methodology and evaluation criteria of data comparison for internal quality control in laboratories of neonatal disease screening. Methods：The internal quality control data of phenylalanine (Phe) in blood were compared and analyzed among 14 neonatal screening sub-central laboratories in Jiangsu province where the same quality control materials were used. The items, including average Phe level (x), standard deviation (SD), standard deviation index (SDI), coefficient of variation (CV), coefficient of variation index (CVI), total error (TE), allowed total error (TEa, critical system error (△SEc), in the laboratories of Jiangsu province were calculated and evaluated. Results：A total of 11 477 lowvalue quality controls were measured, and the qualification percentages of SDI, CVI, CV, TE, △SEc in Jiangsu province were 100%, 57.14%, 42.86%, 78.57%, 14.29% respectively. A total of 11 502 highvalue quality controls were measured, and the qualification percentages of SDI, CVI, CV, TE, △SEc in Jiangsu province were 100%, 35.71%, 92.86%, 100%, 21.43% respectively. Conclusion：The quality control results in most of the laboratories of Jiangsu province met with the requirements of quality controls. The overall mean bias was small, but the statistical results of CV and CVI showed greater imprecision in some laboratories.