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Acute hepatitis C virus (HCV) infection may lead to chronic HCV-infection with detectable HCV RNA or to spontaneous clearance with no HCV RNA, but detectable HCV antibodies. It is unknown whether HCV RNA status is associated with mortality in HIV-infected injection drug users (IDUs). We conducted a nationwide population-based cohort study to examine the impact of HCV RNA status on overall and cause-specific mortality in HIV-infected IDUs. We computed cumulative mortality and used Cox Regression to estimate mortality rate ratios (MRR). We identified 392 HIV-infected patients of whom 284 (72%) had chronic HCV-infection (HCV RNA positive patients) and 108 (28%) had cleared the HCV-infection (HCV RNA negative patients). During 1286 person-years of observation (PYR), 157 persons died (MR = 122/1000 PYR, 95% CI: 104–143). The estimated 5-year probabilities of survival were 0.58 (95% CI: 0.51–0.65) in the chronically HCV-infected and 0.52 (95% CI: 0.40–0.63) in the cleared HCV group. Chronic HCV-infection was not associated with overall mortality: MRR 0.85, 95% CI: 0.59–1.21. In HIV-infected Danish IDUs, chronic HCV-infection is not associated with increased mortality compared to patients who have cleared the infection.