To study the occurrence of hepatitis B virus (HBV) and hepatitis C virus (HCV) in patients with chronic liver disease (CLD) and hepatocellular carcinoma (HCC) in Pakistan, blood samples from 105 sequential patients with biopsy-proven CLD (n = 82) and HCC (n = 23) were tested for HBV and HCV markers. Of the 105, 87 (83%) had evidence of hepatitis B exposure, 58 (55%) were positive for hepatitis B surface antigen (HBsAg), 23 (22%) had hepatitis C antibodies and 25 (24%) had detectable HCV RNA. Significantly more patients with HCC had evidence of HBV exposure in the absence of HCV markers (49/82 vs. 20/23, odds ratio 4·49,95 % CI 1·17–25·16). The proportion of patients positive for HBsAg with no HCV markers was also significantly higher in the HCC group (34/82 vs. 18/23, odds ratio 5·08, 95% CI 1·59—18·96). There were more patients with only HCV markers in the CLD group than the HCC group but the difference was not statistically significant (19/82 vs. 1/23, odds ratio 6·63, 95% CI 0·93—288·01). A modified non-isotopic restriction fragment length polymorphism study on PCR products was used to investigate the epidemiology of HCV genotypes in Pakistan. Due to depletion of the initial samples, a second series of specimens collected one year afterwards was used. Fifteen out of 40 samples had amplifiable product and all were identified as type 3. A commercial serological typing method on the same samples also confirmed that type 3 was the predominant HCV genotype in Pakistan.