To provide effective clinical evidence for prediction and genetic diagnosis, comparison of 3 newborn screening techniques for phenylketonuria and analysis of genetic mutations of infants with positive screening results in Yantai city were performed. Guthrie bacterial inhibition assay, fluorescence immunoassay, and tandem mass spectrometry were used for neonatal screening of PKU in 692,703 dried filter-paper blood specimens. MassARRAY was performed to identify mutant sites in 40 cases of phenylketonuria patients. About 30 neonates with positive Guthrie bacterial inhibition assay results were confirmed to be PKU, 57 with fluorometric testing and 1 with tandem mass spectrometry were observed. Total of 31 different mutations was detected in 40 affected children, with the highest mutation frequency of R243Q. The heterogeneity in genetic mutations among infants with phenylketonuria in Yantai was observed, showing that mutation spectrum differed from those reported in other regions.