HCV spread rapidly throughout the world during the 20th century along multiple transmission routes, including blood transfusion, injection drug use, and unsafe medical injections (Hauri et al., 2004). Our analyses showed limited, if any, partitioning between the isolates identified in this study and collected from GeneBank, indicating that the Pakistani HCV variants represent genotype 3a as broadly as globally circulating variants. This finding suggests strongly that Pakistan, or a larger geographical region that includes it, was where the HCV genotype 3a originated.