This study compared routine analysis for diagnosing Hepatitis C infection by detecting HCV-Ab using ELISA and HCV RNA using qRT-PCR with the detection of Hepatitis C Virus core antigen (HCVcAg) using ELISA. A total of 40 patients and 10 healthy individuals as control were investigated. The data were collected at the time of diagnosis and after the treatment course by Sovaldi, Daklinza, and Ribavirin. At diagnosis, all participants showed positive HCV-Ab and qRT-PCR tests, but about 90% (36 of 40) showed positive HCVcAg. After the treatment course for about six months, all participants showed negative RT-PCR and 73% (29 of 40) showed negative HCVcAg, while all subjects recorded positive HCV-Ab. Three months later, during the repetition of the PCR analysis strategy, nine patients who had received treatment had recovered and showed negative PCR results. Nevertheless, five of the subjects had negative results for HCVcAg, while the other four had positive results. Interestingly, after 6 months, two subjects became positive PCR (relapsed) and four (including the two relapsed patients) became positive core-Ag. Moreover, the correlation analysis showed a positive correlation between RT-PCR data and HCVcAg results. These results suggested a diagnostic marker for detecting HCV infection that might be as accurate as PCR analysis but cheaper, like ELISA.