A group of bacterial protein toxins interfere with vesicular trafficking inside cells. Clostridial neurotoxins affect mainly the highly regulated fusion of neurotransmitter- and hormone-containing vesicles with the plasma membrane. They cleave the three SNARE proteins: VAMP, SNAP-25 and syntaxin, and this selective proteolysis results in a blockade of exocytosis. The Helicobacter pylori cytotoxin is implicated in the pathogenesis of gastroduodenal ulcers. It causes a progressive and extensive vacuolation of cells followed by necrosis, after a cytotoxin-induced alteration of membrane trafficking by late endosomes. Vacuoles originate from this compartment in a rab7-dependent process and swell because they are acidic and accumulate membrane-permeant amines.