Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Hepatitis B or C infections are the main causes of HCC with hepatitis C being the major risk factor for liver cancer in the developed countries. Recently, complications with bacteria of the genus Helicobacter have been associated with HCV-induced HCC. To further understand the mechanisms leading to the development of HCC in the presence of HCV and/or Helicobacter spp., investigation of the differential protein expression in Huh7 cells harbouring HCV-replicon, and replicon cured-Huh7 cells cocultured with H. bilis was done employing two-dimensional gel electrophoresis and mass spectrometry. In the transfected-Huh7 cells exposed to sublethal inoculum densities of H. bilis, 53 different proteins were identified comprising of 28 upregulated and 16 downregulated proteins including 9 potential protein isoforms; in the cured Huh7 cells, 45 different proteins were identified including 33 upregulated, 8 downregulated and, 9 potential protein isoforms. H. bilis affected the modulation of proteins involved in different pathways of Huh7-derived cells physiology including proteins involved in the progression from dysplasia to neoplasm. The result also indicated that the response of the Huh7-derived cells to the presence of H. bilis depended on whether or not HCV replicon was present.