Helicobacter pylori is a human pathogen responsible for severe gastric diseases such as peptic ulcers, gastric adenocarcinoma, and gastric lymphoma. Vacuolating toxin (VacA) is crucial in facilitating the colonization of the gastric lining by inducing cell apoptosis and immune suppression. VacA inserts into membranes and forms a hexameric, anion-selective pore. Here we present a structural model of the VacA pore that strongly resembles the structure of an unrelated anion-selective channel, MscS. In our model, Gly residues in GXXXG motifs pack against small Ala or Val side chains to generate the pore. Our model suggests that the same design of two anion-selective channels was achieved by two different evolutionary paths and provides insight into the mechanism of VacA function.