The aim of this retrospective study was to investigate the infection of hepatitis C virus (HCV) genotypes in hepatocellular carcinoma (HCC) patients from rural areas of Faisalabad region. Among 179 HCC subjects, men and women were 51 and 49%, respectively. All samples positive for HCV RNA by qualitative PCR were genotyped, applying genotype-specific PCR. They were confirmed using HCV 5' non-coding region sequence analytical data. Major risk factor for HCC development and progression was identified to be chronic HCV. It was found among 56.5 ± 2.1 years of age. All these HCC cases were HCV-related and no case was linked with other types of viruses. Using genotype specific primers, HCV genotype 3a (55.3%) was significantly (P<0.0001) higher, followed by 3b (15.8%), 1 (9.24%), 4 (8.05%) and 2 (7.15%). Other genotypes, namely 5a and 6a were only 1.19 and 1.05% among the HCC patients. About 1.05% remained un-typed because of minute viral load. HCV genotype 3a was strongly linked with HCC, followed by 3b. Moreover, HCC was linked with liver cirrhosis (81%). It is suggested that genotyping may be recommended before starting interferon therapy.