In this retrospective study, the data of hepatitis C virus (HCV) markers (anti-HCV and HCV-RNA) obtained from the patients who were prediagnosed and/or diagnosed as HCV infection have been comparatively evaluated and the relationship between these markers and transaminase (ALT and AST) levels have been analysed. A total of 690 sera from patients who were followed-up between January 2002 to December 2004 in Eskisehir Osmangazi University Medical Faculty Hospital were included to the study. Anti-HCV (Axsym System HCV version 3.0, Abbott Laboratories, USA) and HCV-RNA (Real-time Taqman Technology, Roboscreen kit and ABI Prism 7700 Perkin Elmer) tests were studied simultaneously and the results were examined together with the levels of ALT and AST of patients. In our study group, 455 (65.9%) of 690 samples were found positive for anti-HCV, while 235 (34.1%) were negative. Of anti-HCV positive patients, 51.6% (235/455) yielded positive and 48.4% (220/455) yielded negative results for HCV-RNA. The rate of anti-HCV negative but HCV-RNA positive sera was detected as 8.5% (20/235). When liver enzyme levels were taken into consideration, of 690 sera 338 (49%) showed normal transaminase levels, while 352 (51%) had elevated ALT and/or AST levels (23 with increased AST, 57 with increased ALT, and 272 with increased ALT and AST). Of the patients who exhibited increased ALT+AST levels (n=272), 50% were found positive for both markers (anti-HCV and HCV-RNA), 17% were only positive for anti-HCV, 3.6% were only positive for HCV-RNA, and 29% were negative for both markers. As a result, since anti-HCV negativity may be detected in viremic patients, molecular methods should be applied especially for the diagnosis of suspected cases and cases without seroconversion.