ObjectiveTo establish a hereditary deafness genetic screening cohort and conduct prospective follow-up to evaluate the effectiveness of the Nantong newborn genetic deafness screening program. MethodsA study based on traditional screening of newborn hearing was conducted from January 2016 to June 2021. Newborns in six hospitals in Nantong were screened for 15 hotspot mutation loci in four common deafness genes. Cohort follow-up was conducted. ResultsA total of 40 403 newborns were included, with a carrier rate of 39.5 per 1 000 for the four common deafness genes. In total, 168 children with hearing loss (HL) were identified at screening and follow-up, of which 56.5% (95 cases) had severe or very severe HL. The detection rate of HL was significantly higher with combined screening than with traditional screening (3.0‰ vs. 3.9‰, P<0.001). All four carriers of pathogenic mutations with normal hearing developed late-onset HL within 2 years of age. At the end of follow-up, six of the polygenic heterozygous mutation carriers had congenital HL and five had late-onset HL. Carriers of polygenic heterozygous mutations were more common as compared to other carrier mutation populations (2.1% vs. 68.8%, P<0.001). In addition, 525 carriers of the SLC26A4 mutation and 118 carriers of the MT-RNR1 mutation were identified and their parents were counselled during the combined screening, and no children with HL was identified during the follow-up period. ConclusionGenetic screening for deafness improves the detection of HL at birth. It is recommended that carriers of pathogenic mutations with normal hearing at birth be followed up every 3 to 6 months until the age of 2 years. Carriers of polygenic heterozygous mutations should undergo extended screening for deafness genes and have their hearing monitored more intensively for early detection of late-onset or progressive HL.