The experience of treatment for hepatitis C virus genotype 6 (HCV-6) was limited in Taiwan due to rare incidence in general population and lack of medical care in the correction facilities where HCV-6 was endemic. This work was to investigate the response of treating HCV-6 incarcerated injection drug users (IDU), compared with HCV-1 incarcerated IDUs. 106 inmates completed treatment and follow-up (39 HCV-6, 67 HCV-1, cirrhosis or co-infection with hepatitis B virus or human immunodeficiency virus excluded) were enrolled in this retrospective study among 182 registered peginterferon/ribavirin therapies of National Health Insurance (NHI) reimbursement in the Kaohsiung and Pingtung correcting facilities from 2014 to 2017. Among the 67 HCV-1 and 39 HCV-6 patients, there was no difference with regard to patient’s demographics, hemogram, baseline HCV viral load, except for a higher alanine aminotransferase (ALT) level in HCV-6 patients than HCV-1 patients. Afterword, a higher rapid viral response (RVR) was noted in HCV-6 (64% vs 41%, p=0.018), the sustained viral response (SVR) in HCV-6 or HCV-1 patients who received at least one dose of treatment and the patients who completed the full course of treatment were comparably excellent, (100% vs 89%, p=0.16) and (100% vs 91%, p=0.19) respectively. Although interferon-free direct acting antiviral agents (DAA) are the mainstay of therapy in the world, the peginterferon/ribavirin may be an alternative option for the incarcerated IDU patients with HCV-1 or HCV-6 infection, based on the excellent SVR rate and the limited governmental support for DAA treatment.