Bacterial virulence factors and secreted extracellular proteins from damaged host cells following infection have been recognized as key mediators in the pathophysiological alterations observed in septic shock, and have also been shown to have a synergistic influence on bacterial pathogenicity. We hypothesized that during infections, virulence factors as well as host-shed proteins may synergistically influence aspects of the pathogenicity of V. vulnificus, such as primary septic shock and overproduction of proinflammatory cytokines. However, virulence factors and host-derived proteins have yet to be clearly evaluated during V. vulnificus infection. In this study, we analyzed and compared the proteins in conditioned supernatants generated from co-cultures of host cells and either wild-type or rtxE mutant V. vulnificus using LC-QTOF-MS/MS analysis. In a previous study, we determined that the culture supernatants of the rtxE mutant V. vulnificus-infected INT-407 cells induced significantly lower levels of IL-8 production from human intestinal epithelial cells than did the culture supernatants of wild-type V. vulnificus-infected INT-407 cells. LC-QTOF-MS/MS analysis results demonstrated that levels of proteins such as HSP90 α/β, 14-3-3 γ, PRX II, hnRNP K, β-actin, α-tubulin and V. vulnificus flagellin were significantly lower in the culture supernatants of rtxE mutant V. vulnificus-infected INT-407 cells than in the culture supernatants of wild-type V. vulnificus-infected INT-407 cells. These results demonstrate that V. vulnificus RTX toxins acting via rtxE, a transporter of virulence factors, play a very important role in the pathogenesis of V. vulnificus, as well as in its initial role in inducing pathogenic mediators from host cells.