Clinical research suggests a role for viral load measurement in predicting and monitoring Epstein-Barr virus (EBV)-associated diseases. The aim of this study was to assess the performance of the recently commercially available quantitative assays for EBV based on real-time PCR: the RealArt EBV LC PCR kit and the LightCycler EBV quantification kit. A total of 87 samples were analyzed: 67 samples were obtained from transplant recipients and patients with EBV-associated diseases, 8 samples were obtained from the Quality Control for Molecular Diagnostics 2002 EBV Proficiency Program, and 12 negative qualitative nested PCR samples were used as negative controls. Inter-and intra-assay variabilities were determined by running replicates of two samples. All samples were run in a LightCycler instrument. The differences between positive and negative results were not considered statistically significant (P ؍ 0.5355). There were no false-positive results using either method for nested PCR negative-control samples. The difference in viral load values using the two different methods was considered statistically significant (P < 0.01). The logarithmic linear correlation for both assays was low (r ؍ 0.449) but significant (P < 0.01). The LightCycler EBV quantification kit showed a wider dispersal in results but produced substantially more-accurate melting temperature profile curves. The bias towards lower measurements was considerable in comparison with higher viral load. The differences in PCR efficiency and the presence of mutations could explain the disparity between the two methods. It was concluded that confidence intervals would be required to report the results rather than plain absolute values of viral load for patient monitoring.Epstein-Barr virus (EBV) is a human herpesvirus included in the Gammaherpesvirinae subfamily and is the only human species belonging to the genus Lymphocryptovirus (11). EBV infects more than 90% of the world's population, leaving the majority of individuals with a lifelong silent infection (14). Although most primary EBV infections are asymptomatic, the virus is the causative agent of infectious mononucleosis, a mild and self-limited lymphoproliferative disease (13). EBV is associated with the development of two epithelial tumors, nasopharyngeal carcinoma (5) and oral hairy leukoplakia, seen mainly in human immunodeficiency virus infection (3), as well as with various lymphoid carcinomas, lymphoproliferative disease in immunosuppressed patients, Burkitt's lymphoma, Hodgkin's disease, and T-cell non-Hodgkin's lymphoma (25).EBV DNA is present in a small fraction of lymphoid cells, and healthy virus carriers harbor 1 to 50 EBV genomes per 10 6 mononuclear cells, with B lymphocytes representing the major cellular reservoir (9). Qualitative PCR assays are unable to distinguish between active and latent infection. Consequently, clinical interpretation of positive results is difficult. However, clinical research suggests a role for viral load measurement in predicting and monitoring EBV-associate...