Human cytomegalovirus infection is highly prevalent in Indian population. It is the commonest congenitally acquired infection causing various anomalies. The diagnosis of infection in neonates is difficult as IgM may not be detected in all cases. The polymerase chain reaction is reported as alternative and better option in these patients. However, there is lack of data to substantiate this preference in a resource poor country like India.Blood samples from 930 neonates/fetuses were first tested for specific anti-CMV IgM antibodies using mu-capture enzyme linked immunosorbent assay, Mac-ELISA. Nested PCR was first standardised on clinically and therapeutically confirmed cases of CMV disease. In the second phase blood samples randomly from 20 babies suspected of CMV infection were collected for serology and PCR and both tests were run independently. Twenty healthy controls were also included. IgM ELISA and PCR were performed on these samples and results of these 20 samples were compared to evaluate the sensitivity and specificity of each method.Out of 930 serum samples of suspected congenital CMV infection 188 (20.2%) were found positive for CMV specific IgM antibodies. While comparing the results of 40 paired samples, PCR was found to be highly specific (100%) but less sensitive than Mac-ELISA (95%) with negative predictive value of 100% and positive predictive value of 95%. Thus in congenital CMV infection Mac-ELISA was less costly, less cumbersome and more user friendly.The Mac-ELISA seem to have parallel sensitivity and specificity as PCR for diagnosing congenital CMV infection.