Hsp100/Clp proteins are key players in the protein quality control network of prokaryotic cells and function in the degradation and refolding of misfolded or aggregated proteins. Here we report the identification of a new class of Hsp100/Clp proteins, termed ClpV (virulent strain), that are present in bacteria interacting with eukaryotic cells, including human pathogens. The ClpV proteins are most similar to ClpB proteins within the Hsp100/Clp family, but cluster in a separate phylogenetic tree with a remarkable distance to ClpB. ClpV representatives from Salmonella typhimurium and enteropathogenic Escherichia coli form oligomeric assemblies and display ATP hydrolysis rates comparable to ClpB. However, unlike ClpB, both ClpV proteins failed to solubilize aggregated proteins. This lack of disaggregation activity correlated with the inability of ClpB model substrates to stimulate the ATPase activity of ClpV proteins, indicating differences in substrate selection. Furthermore, we show that clpV genes are generally organized in a conserved gene cluster, encoding a potential secretion system, and we demonstrate that increased levels of a dominant negative variant of either S. typhimurium or Yersinia pseudotuberculosis ClpV strongly reduce the ability of these pathogenic bacteria to invade epithelial cells. We propose a role of this novel and unique class of AAA+ proteins in bacteria-host cell interactions.