Hepatitis C virus (HCV) is a global health problem and one of the main reasons for chronic liver disease like cirrhosis and hepatocellular carcinoma. The HCV genome is translated into a polyprotein which is proteolytically processed into ten viral proteins. The interactome of the HCV proteins with the host cell has been worked out, however it remains unclear how viral proteins interact with each other. We aimed to generate the interaction network of these ten HCV proteins by a flow cytometry based FRET assay established in our laboratory (Banning et al, 2010 PLoS ONE 5(2): e9344). HCV proteins were constructed as fusions with the chromophores CFP and YFP. All HCV fusions were expressed and localized to specific subcellular compartments, indicating that they are functional. FACS-FRET measurements identified a total of 20 interactions. 13 of these were previously described and are now confirmed by our method in living cells. Among the seven novel protein binding pairs HCV p7 plays a pivotal role. It binds to the HCV capsid protein Core and the two glycoproteins E1 and E2. These interplays were further demonstrated in the relevant context of Huh7.5 liver cells expressing infectious HCV. Our work demonstrates the feasibility to rapidly generate small interaction networks by FACS-FRET and defines the network of intra HCV protein interactions. Furthermore, our data supports an important role of p7 in HCV assembly.