Evaluation of the human immunodeficiency virus type 1 (HIV-1) copy number in plasma (viral load) is essential to monitor the kinetics of the viral replication in infected individuals and is used in clinical diagnostics. The object of this study was to determine the number of HIV-1 copies in plasma of infected individuals using two standard molecular assays and to compare the results in order to evaluate compatibility of these assays. The COBAS® AmpliPrep/COBAS® AMPLICOR HIV- 1 MONITORTM, version 1.5 Test is standard assay used in clinical laboratories and is based on the traditional PCR technology. The new COBAS® AmpliPrep/COBAS® TaqMan® HIV-1 test is based on the technology of the real-time PCR and is available since 2008. Viral load was measured in plasma samples of 64 HIV-1 infected individuals. Viral load measured with traditional PCR (mean 4.2 log10 copy/ml) showed greater statistical discrepancies compared to viral load from real-time PCR (mean 3.73 log10 copy/ml). The correlation coefficient of the assays was only 0.74. Out of 64 samples, 23 gave results with variances greater than 5 log10 copy/ml plasma, which is our clinical cutoff. The results of this study showed that the new real-time PCR assay analytically undermines the number of HIV-1 RNA copies in plasma and that its results cannot be compared to the results of the traditional PCR.