Cytomegalovirus(CMV) infection may be acquired congenitally, perinatally or postnatally in babies.Congenital and perinatal  CMV infection  can be diagnosed by  viral  culture or detection and quantitation  of CMV DNA by RealTime QuantitativePCR (RT–qPCR) in blood ,urine and body fluids..The objective of this study was  to diagnose and determine CMV  load in infants presenting with clinical features suggestive of cytomegalovirus infection byRT–qPCR of urine.Thisdescriptive study was done on babies admitted to the Departments of Neonatology and   Paediatrics Govt Medical College,Kozhikode from January 2016–December 2017.Urine samples from 142 babieswere received  and processed   in the Microbiology Department.  DNA isolation and amplification was performed   using  commercial DNA extraction kit and PCR kit for detection  and quantification of CMV. Serum samples of the babies  withCMV viruria were tested  for CMV IgM antibodies.Of 142 babies  suggestive of CMV infection CMV–DNA was detected and quantitated  in urine of 25(17.60%) (mean age 3.36 months). .CMV IgM was  positive in 15/25(60%) babies with viruria.Twenty two had congenital CMV infection (cCMV) and 3 had perinatal infection.The most common clinical presentation was jaundice13( 52%).Of 8 babies started on Ganciclovir  7 responded to treatment.RT–qPCR helps in diagnosing and quantitating CMV load which  helps in  deciding on therapy and assessing response to treatment,and can predict risk for longterm sequelae.