Abstract Background Cytomegalovirus (CMV) remains a major opportunistic agent among transplant recipients. While detection of CMV pp65-lower matrix protein (pp65Ag) is still widely used for monitoring CMV infection, real-time PCR assays have been recently developed for routine quantitation of CMV DNA. However, correlations are lacking between results of pp65Ag and quantitative PCR assays and there is no consensus yet as to the more appropriate blood compartment (whole blood (WB), leukocytes, plasma) to be tested with PCR assays. Objectives The aims of the study were to determine, in a population of transplant recipients: (i) the correlation between pp65Ag and CMV quantitative real-time PCR in our setting and (ii) the utility of plasma CMV DNA quantitation in comparison to WB quantitation. Methods In 170 blood samples (from 61 solid organ or bone marrow transplant recipients) with pp65Ag results, CMV quantitation was performed in WB and plasma using an in-house real-time quantitative PCR. Results Real-time PCR and pp65Ag results in WB were correlated: thresholds of 10 and 50(+) cells/200,000 cells were equivalent to 3.3 log 10 copies/mL (2000 copies/mL) and 3.8 log 10 copies/mL (6300 copies/mL), respectively. When WB viral load was ≥3.6 log 10 copies/mL, the risk to have a negative plasma CMV DNA result was ≤2.5%. Conclusions For the routine exploration of a single compartment, whole blood would represent a suitable compromise: easy processing for a sensitive assay. The 3.6 log 10 copies/mL threshold, which could help in identifying active CMV infection, deserves further evaluation.