It is necessary to use rapid and reliable methods for the diagnosis of hepatitis C virus (HCV) infections and follow up of the patients with HCV infection. The purpose of this study was to compare Cobas Amplicor system (Roche Diagnostics) and Cobas Taqman system (Roche Diagnostics) for the quantitative detection of HCV-RNA in clinical samples. Eightyfour serum samples that were sent to Hacettepe University Adult Hospital Clinical Microbiology Laboratory were included in the study. Fiftytwo (61.9%) of these samples were found to be positive by two methods while 32 (38.1%) samples were found to be negative by two methods. There were no discrepant results between the methods. When positive samples were evaluated it was found that Cobas Amplicor system detected an average HCV-RNA of 822.452 IU/ml while Cobas Taqman system detected an average HCV-RNA of 3.069.984 IU/ml. Since the mean number of HCV-RNA detected by Cobas Taqman system was 3.7 fold of the average number of HCV-RNA detected by Cobas Amplicor system, it was concluded that Cobas Taqman system was a reliable method for the follow up of patients with HCV infection.