The aim of this study was to investigate the concordance between COBAS Taqman 48 (Roche Molecular Systems, Pleasanton, CA, USA) and VERSANT HCV RNA 3.0 (Bayer Diagnostics, Terrytown, NY) test systems for the detection of hepatitis C virus (HCV) load. Plasma samples taken from 42 patients with chronic HCV infection between 15 May-15 June 2006, were included to the study, and HCV-RNA levels have been searched with the use of the two above mentioned systems. Thirteen of the samples (30.9%) yielded negative and 26 (61.9%) samples yielded positive results by both of the systems. Two samples that were found negative by COBAS system, displayed 3.38 and 3.41 log10 IU/ml HCV-RNA by VERSANT system, respectively, while one sample that was found negative by VERSANT system, displayed 2.52 log10 IU/ml HCV-RNA by COBAS system. The correlation and linearity of the tests were found high according to Pearson correlation analysis [(r = 0.904, p < 0.0005), (R2 = 0.817)]. The viral load values detected by COBAS AmpliPrep/COBAS Taqman 48, were higher than the values obtained by VERSANT HCV-RNA 3.0, with a mean of 0.33 log10 IU/ml. In conclusion, both of the systems yielded similar results, however, since HCV viral load values may differ in different systems, the follow-up of viral load should be done by the same system for a particular patient.