BACKGROUND AND PURPOSE: Hepatitis C virus (HCV) co-infection's role on cognitive impairment of human immunodeficiency virus (HIV) positive patients is still debated and functional neuroimaging evaluation on this matter is lacking. To provide further insight about HCV's neuro-effects on HIV associated neurocognitive disorder (HAND), we performed a pilot resting state (RS) functional connectivity magnetic resonance imaging (fcMRI) study to find eventual functional connectivity alteration that could reflect HCV related cognitive performance degradation. METHODS: Eighteen patients (8 HIV, 10 HIV + HCV), either impaired or not impaired, were assessed with RS fcMRI. A statistic model including cognitive testing results was elaborated during data processing to evaluate brain networks alteration related to actual cognitive status in patients. RESULTS: Statistically significant different patterns of connectivity were found: HCV co-infection modified 17 ROIs' connectivity with 45 supra-threshold connections (p-FDR min 0.0022, max 0.0497). ROIs most involved were right pallidum, brainstem, vermian lobules 1-2 and right cerebellar lobule 10. Graph theory analysis did not demonstrate significant difference between networks, but HCV related modifications at ROI's local level were found, with particular involvement of ROIs of frontal lobe, basal ganglia and cerebellum. Increased fronto-striatal dysfunctions have been already reported as consequences of HCV infection and could reflect an additive effect. Cerebellar alterations are associated with HIV and HAND, but not with HCV infection, suggesting a synergic effect of HCV. CONCLUSION: Our study demonstrates RS fcMRI can help to understand the interactions between HIV and HCV co-infection, and our preliminary results suggest synergic effects of HCV in HIV-related brain functional modification.