Injecting drug use is associated with an increased risk of blood-borne viral infections, such as hepatitis B and C viruses (HBV and HCV, respectively) and human immunodeficiency virus (HIV). However, their prevalence, virological characteristics, and associated factors are not clear among the injecting drug users in Korea. The aim of this study was to determine the prevalence of HBV, HCV, and HIV infection, as well as their virological and clinical characteristics of injecting drug users in South Korea. Between 2007 and 2010, 318 injecting drug users (89.3% male; mean ± age 41.9 ± 8.15 years) were participated. While HIV infection was not found, the seroprevalence of anti-HCV and HBV surface antigen (HBsAg) was 48.4% (n = 154) and 6.6% (n = 21), respectively. HBV/HCV co-infection was found in 4.1% (n = 13). Occult HBV infection was suggested in 5.0% (n = 16). Among the HCV genotypes, 1b (37.7%) and 2a/2c (35.7%) were mostly often detected. HCV RNA was detected in 98.1% (n = 151/154) and high-level viremia (HCV RNA level, ≥400,000 IU/ml) were observed in 59.6% (n = 90/151). In multiple logistic regression analysis, old age (OR 1.18 per year, 95% CI = 1.09-1.27) and ever-sharing injecting equipment (OR 4.17, 95% CI = 1.39-12.45) independently predicted HCV mono-infection. The prevalence of HBV and HCV infection were high but largely undiagnosed in the present sample of Korean injecting drug users. Strategic prevention, screening, and treatment are needed to reduce further transmission and morbidity.