The clinical manifestations in cytomegalovirus infected-infants vary from asymptomatic illness to highly fatal cytomegalic inclusion disease. The influence of human cytomegalovirus (HCMV) strains on the outcome of HCMV disease is poorly explored. The present study was undertaken to explore the role of gB genotypes with clinical features in infants with clinically suspected HCMV disease. Urine samples of 71 infants (age < 1 year) with clinically suspected HCMV disease were subjected to amplification of glycoprotein B (gB) gene by polymerase chain reaction (PCR) followed by restriction fragment length polymorphism using RsaI and HinfI. HCMV DNA could be detected in 12 samples by gB gene PCR, 6 of which comprised of gB2, followed by gB1 in 5 samples and gB3 in 1 sample. Organomegaly was the most common finding (67%) followed by jaundice (50%), pneumonia (50%), seizures (42%), microcephaly (25%), low birth weight (25%) and rashes (17%). No particular genotype was significantly associated with specific clinical presentation or organ system involvement.