The aim of this study was to determine the geographical distribution of hepatitis C virus genotypes/subtypes among people who inject drugs (PWID) recruited at 22 needle exchange sites and drug outpatient services in all seven Planning and Statistical Regions of Hungary. Of 198 such PWID, 147 (74.2%), 45 (22.7%) and six (3.0%) carried genotype 1, 3 or 4, respectively, and 31 (72.1%) of the 43 genotype 1 sequences were of subtype 1a. Genotype 3 was significantly more prevalent in provincial towns than in the capital, Budapest. Injecting for a longer period and an older age both correlated with a higher prevalence of genotype 3, suggesting possible future changes in genotype distribution. The distributions of hepatitis C virus genotypes/ subtypes differed significantly between the tested PWID and the general population. The identification of genotype 3 reflected its worldwide occurrence among PWID. Our results underline the importance of genotyping before treatment, especially among people who have ever injected drugs in Hungary.