Co-infection with hepatitis B and C among HIV infected patients are prevalent among high-risk populations. This meta-analysis aimed to estimate the prevalence of HIV, HCV and HBV co-infections among high-risk populations in Iran. We systematically searched the national and international electronic databases until 2016. The primary outcome was the prevalence of HIV, HBV, HCV and HIV co-infections in different high-risk populations in Iran. All English and Persian studies conducted on Iranian high-risk groups were included in the study. The review was reported based on PRISMA guidelines and data were analysed at 95% confidence level using random effect models. Overall, 916 relevant papers were recognised and 14 articles were included in the meta-analysis. The pooled estimates of HBV/HCV, HCV/HIV, HBV/HIV and HBV/HCV/HIV were 1.3% (95%CI: 0.5-2.1), 16.3% (95%CI: 1.1-31.6), 0.5% (95%CI: 0-1.4) and 0.5% (95%CI: 0.2-0.8), respectively. Based on subgroup analysis, there was a higher proportion of all co-infections from the years 2010-2016 as compared to that of the years 2003-2009. Our results highlighted that HCV/HIV co-infection in Iranian high-risk groups including injection drug users (IDUs) and prisoners is common. In addition, the increasing trend of coinfections should be considered alarming for policymakers.