RNA interference (RNAi) has been widely used for the analysis of gene function and represents a new promising approach to develop effective antiviral drugs. In this study, several small interfering RNAs (siRNAs) corresponding to two structural genes (core and E2) of hepatitis C virus (HCV) were designed and in vitro transcribed to explore the possibility of silencing these two genes. The plasmids pEGFP-C and pEGFP-E2, which contain the EGFP reporter gene and the core or E2 gene as silencing targets, were co-transfected with siRNAs into HEK 293T cells. At various time points of post-transfection, core and E2 expression levels were detected by fluorescence microscopy, flow cytometry, Western blotting, and real-time quantitative PCR. The results showed that the mean fluorescence intensity, protein expression, and RNA transcripts of siRNAs transfected cells were significantly reduced. This may provide an approach for the development of novel prophylactic or therapeutic agents for HCV infection.