The hepatitis C virus (HCV) RNA replication complex (RC), which is composed of viral nonstructural (NS) proteins and host cellular proteins, replicates the viral RNA genome in association with intracellular membranes. Two viral NS proteins, NS3 and NS5A, are essential elements of the RC. Here, by using immunoprecipitation and fluorescence resonance energy transfer assays, we demonstrated that NS3 and NS5A interact with tubulin and actin. Furthermore, immunofluorescence microscopy and electron microscopy revealed that HCV RCs were aligned along microtubules and actin filaments in both HCV replicon cells and HCV-infected cells. In addition, the movement of RCs was inhibited when microtubules or actin filaments were depolymerized by colchicine and cytochalasin B, respectively. Based on our observations, we propose that microtubules and actin filaments provide the tracks for the movement of HCV RCs to other regions in the cell, and the molecular interactions between RCs and microtubules, or RCs and actin filaments, are mediated by NS3 and NS5A.Hepatitis C virus (HCV) is a major causative agent of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. The positive-sense, single-stranded 9.6-kb RNA genome encodes a large polyprotein (Ͼ3,000 amino acids), which is processed by host and viral proteases into 10 structural and nonstructural (NS) proteins (17, 34). Most of the NS proteins (NS2, NS3, NS4A, NS4B, NS5A, and NS5B) of HCV were associated with the endoplasmic reticulum (ER) or other subcellular membranes when these proteins were expressed individually or as a polyprotein (23,24,40,52), with the probable exception of NS2, and are involved in HCV RNA replication (4,35,43). NS3 is a helicase and a serine protease, with the latter requiring a cofactor, NS4A. It is conceivable that the enzymatic activities of these proteins are key elements of the HCV replication complex (RC). The NS4B protein alone induces the membranous web in a membranous matrix; the newly synthesized HCV RNA also exists in these membranous webs (12, 16). NS5A is a phosphoprotein and an essential component of the HCV RC and plays an indispensable role in viral replication (4). NS5B is an RNA-dependent RNA polymerase. All of these NS proteins and the replicating HCV RNA, together with host proteins, are believed to form a membrane-associated HCV RC. We have further shown that HCV RNA synthesis occurs in a lipid raft membrane structure (2, 47). However, the full content and mechanisms of replication of HCV RC remain unclear.Our previous studies have shown that vesicle-associated membrane protein-associated protein (VAP) subtype A (VAP-A) and VAP subtype B (VAP-B) bind to both NS5A and NS5B and play a critical role in the formation of HCV RC