OBJECTIVE: To explore the cost-effectiveness of the diagnosis of congenital cytomegalovirus (CMV) infection by fluorescent quantitative polymerase chain reaction (FQ-PCR) in neonates. METHODS: Serum CMV immunoglobulin M (CMV-IgM) and CMV-IgG were detected using ELISA in 610 neonates aged less than 14 days. CMV DNA content was detected by FQ-PCR. The cost-effectiveness analysis was then performed. RESULTS: The positive rate of FQ-PCR in neonates with positive CMV-IgM was 42.9% (15/35), while, 2.9% (16/547) in neonates with positive CMV-IgG. The mean logarithm values of CMV DNA in neonates with positive CMV-IgM were higher than those in neonates with positive CMV-IgG (5.79±1.24 vs 4.11±0.87; P<0.01). The costs of the diagnosis of CMV infection by FQ-PCR were 256 RMB/case in neonates with positive CMV-IgM, and 3 760 RMB/case in neonates with positive CMV-IgG. CONCLUSIONS: The CMV DNA content in neonates with positive CMV-IgM is higher than that in neonates with positive CMV-IgG. Diagnosis of congenital CMV infection by FQ-PCR in neonates with positive CMV-IgG is not suitable for large scale epidemiological survey because of high cost-effectiveness ratio.［Chin J Contemp Pediatr, 2010, 12 (10):796-798］