Standardized protocols and methods for virological monitoring are mandatory for the correct surveillance of human cytomegalovirus (HCMV) infection in transplanted patients receiving pre-emptive therapy. Fifteen Italian viral diagnostic laboratories belonging to different transplantation centers participated in the external Quality Control Programme for Molecular Diagnostics of HCMV-DNA by using two in-house and five commercial methods for HCMV-DNA quantification. The different methods shared 100% specificity, and sensitivity reached 100% when samples containing > 1,000 copies/ml were considered. The variability range was wide (about 2 log10) for samples containing a lower amount of HCMV-DNA (< 1,000 copies/ml), but it decreased with increasing concentrations of HCMV-DNA. For HCMV-DNA levels > or = 5,000 copies/ml, the different methods provided results within a +/- 0.5 log10 variability range, while the 80% range (range in which 80% of results obtained will fall) was within +/- 0.3 log10 or less. An acceptable level of variability was reached among different in-house and commercial methods for HCMV-DNA quantification in samples containing a clinically significant viral DNA amount. Based on these data, standardized cutoffs established for pre-emptive therapy in different transplantation centers should provide comparable clinical and virological results among centers.