BACKGROUND Cytomegalovirus (CMV) infections are an important cause of morbidity and mortality in transplant recipient. To date, the antigenemia assay is the most used technique for diagnostic and management of CM V infections. However, quantification of CMV viral load by real time polymerase chain reaction (RT-PCR) has becoming the method of choice to detect CMV in a rapid, sensitive and specific manner. OBJECTIVE To compare antigenemia and RT-PCR assays in the detection of CMV in blood sample from solid organ and bone marrow transplant (BMT) in children attended at the Dr. Luis Calvo Mackenna Hospital. METHODS In a prospective study, we detect the presence of CMV in blood sample by RT-PCR and antigenemia assays. RESULTS We analyzed 219 blood samples from 68 children subjected to kidney, liver and BMT. Out of 219 samples analyzed, 147 were negative and 33 were positive for CMV by both techniques. Thirty-seven samples were positive only by RT-PCR and 2 by antigenemia. Considering the antigenemia as a reference, RT-PCR shows 94%, 80%, 34% and 99% sensitivity, specificity, positive and negative predictive values, respectively. The kappa coefficient between both techniques was 0.528. CONCLUSIONS Quantitative determination of CMV viral load by RT-PCR is a sensitive technique with excellent negative predictive valué compared to antigenemia. Our results support the use of RT-PCR as a technique that might facilítate the diagnostic and treatment of active CMV infection in pediatric transplants.