Abstract: Objective To understand the mutation type and mutation carrying rate of the common deafness genes of the newborn in Nanning City, evaluate the detection results of deafness genes, and provide the basis for the long-term prevention and clinical diagnosis of hereditary deafness. Methods A total of 42 708 newborns were collected in Obstetric, Paediatric Clinic and Otolaryngology Clinic of Guangxi Maternal and Child Health Hospital from January 2016 to December 2018. Four common genes in China were screened by Matrix assisted laser desorption ionization time of flight mass spectrometry, including 20 mutation loci of GJB2(35 delG, 176-191 del16, 167 delT, 299_300 delAT, 235 delC), GJB3(538 C>T, 547 G>A), SLC26 A4(281 C>T, 589 G>A, 1174 A>T, 1226 G>A, IVS7-2 A>G, 1229 C>T, 1975 G>C, 2162 C>T, 2027 T>A, IVS15+5 G>A, 2168 A>G), and Mt12 SrRNA(1555 A>G, 1494 C>T). Results Among 42 708 newborns, 940 had gene mutation, with a total positive detection rate of 2.201%, including 492 GJB2 mutations(1.152%), 61 GJB3 mutations(0.143%), 320 SLC26 A4 mutations(0.749%) and 57 Mt12 SrRNA mutations(0.133%). Meanwhile 1 compound heterozygote and 9 double heterozygotes were founded. Conclusion In this study, GJB2 and SLC26 A4 were the major mutations, and 235 delC and IVS7-2 A were the major loci. The combined screening of newborn hearing and deafness gene is important to prevention of deafness, especially the prevention of drug-induced deafness, and is the great significance in reducing the occurrence of deafness and birth defects.