Hepatitis C virus (HCV) infection occurs among human immunodeficiency virus (HIV)-infected men who have sex with men (MSM) because of shared routes of transmission. To assess the association between HCV and HIV infection among MSM in Peru, we conducted a matched case-control study (162 HIV-positive cases and 324 HIV-negative controls) among participants of an HIV sentinel surveillance survey in six urban cities. The HCV infection was initially screened using anti-HCV ELISA and immunoblot assay, and thereafter confirmed by the HCV RNA qualitative assay. Among cases, no confirmed HCV infection was found while among controls, only two confirmed HCV infections were reported (0.62%). This matched case-control reports a very low probability of association between HCV and HIV co-infection and suggests a very low prevalence of HCV infection among MSM in Peru.