Background: Prevention and early treatment of congenital CMV infection have a high priority in our country. The main goal of this study was to search the CMV Ag65 in blood and CMVDNA (PCR) in perilymphatic fluid of children undergone to cochlear implant surgery. Methods and materials: A cross sectional study (2012-2014) designed in Rasoul Akram hospital referral centre in Tehran, Iran. Thirty nine cases with cochlear implant surgery (mean age=2.37+2.16 years) evaluated for CMV infection. One ml of the whole blood were obtained from cases before surgery and searched for CMV antigen p65. Also perilymphatic fluid were taken during surgery and searched for CMV-DNA by PCR method. The results compared. Chisquare values (CI: 95%; P<0.05) were calculated. P value<0.05 was considered significant. Results: Positive CMV-Ag 65 detected in 43% (18/39), positive CMV-PCR were found in 26.7% (10/39) of cases. A poor agreement was found between 2 methods for CMV infection in cases. Sensitivity and Specificity, PPV and NPV for CMV antigenemia (p65) in compare with positive CMV DNA (PCR) in perilymphatic fluid were 43%, 54%, 77% and 65%, respectively. The mean age of cases with positive and negative CMV PCR was meaningful (p?0.001) but not for CMVantigen p 65 (p=0.3). No correlation between positive CMV results (both methods) and positive clinical signs for CMV infection (except SNHL) were observed (p=0.4, 1). Conclusion: Universal screening of newborns for congenital CMV and longitudinal audiometric follow-up are needed for all confirmed CMV infected cases. We prefer to consider CMV seropositive SNHL children (<1 year old) as congenital form. We recommend a complete DNA assay in blood for CMV infection to differentiate the congenital from the acquired infection in seropositive (CMV-IgM) cases after first birth day. Treatment of CMV infection can diminish occurrence of SNHL.