This invention relates to compounds, compositions, and methods useful for modulating Hepatitis C Virus (HCV) gene expression using short interfering nucleic acid (siNA) molecules. This invention also relates to compounds, compositions, and methods useful for modulating the expression and activity of other genes involved in pathways of HCV gene expression and/or activity by RNA interference (RNAi) using small nucleic acid molecules. In particular, the instant invention features small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules and methods used to modulate the expression of HCV genes, including cocktails of such small nucleic acid molecules and lipid nanoparticle formulations of such such small nucleic acid molecules cocktails thereof. The application also relates to methods of treating diseases and conditions associated with HCV gene expression, such as HCV infection, hepatocellular carcinoma, cirrhosis, liver failure, as well as providing dosing regimens and treatment protocols.