Objective We aimed to investigate DNA damage level and new potential biomarkers that can assist the diagnosis and treatment of congenital hearing loss. Design A prospective, non‐randomized study. Setting Canakkale Onsekiz Mart University, Canakkale, Turkey Participants We included a patient group consisting of 17 patients with congenital hearing loss and a control group consisting of 17 healthy individuals. Main outcome measures We applied the brainstem-evoked response audiometry (BERA) tests to determine the hearing loss. After taking blood samples, we applied cytokinesis-block micronucleus cytome (CBMN) assay. Methods After the demographic characteristics, family stories and Brainstem Evoked Response Audiometry results of both groups were obtained, their blood was taken. The cytokinesis-blocked micronucleus assay technique was applied to the blood samples to measure the frequency of micronucleus, nucleoplasmic bridge, and nuclear bud in both groups. Results We observed that the micronucleus, nucleoplasmic bridge, and nuclear bud frequencies were found to be significantly higher in hearing loss patients than the control group (p<0.0001). Also, we observed that the frequency of micronucleus in hearing loss patient was positively correlated with nuclear bud, which may indicate a common mechanism for these endpoints. Conclusion It was, for the first time, demonstrated that micronucleation, nucleoplasmic bridge, and nuclear bud formation were found to be higher, which is an indication of genomic instability in patients with congenital hearing loss. Since the markers we evaluated were linked with crucial diseases, our findings might suggest that patients are susceptible to many crucial diseases, including cancer.