The recent surge in injection drug use (IDU) in Prague, Czech Republic, provided an opportunity to compare the distribution of hepatitis C virus (HCV) genotypes among recent injection drug users and nonusers. We provide evidence that the most common HCV subtype, 1b, has been circulating in Prague longer than the other subtypes but that IDU practice has magnified its recent prevalence, and that the primary drug of choice among IDU subjects appears to influence the prevalence of a particular HCV subtype.