Helicobacter pylori broth culture supernatants induce eukaryotic cell vacuolation in vitro, a phenomenon that has been attributed to cytotoxic activity. We sought to characterize further the vacuolation of HeLa cells that occurs in response to H pylori culture supernatant. Nascent vacuoles were detectable by electron microscopy after 90 minutes of incubation with H pylori supernatant and were not associated with any identifiable organelle. After 6 days of incubation with H pylori supernatant, vacuoles were membrane-bound structures filled with electron-dense debris, which resembled secondary lysosomes. Acid phosphatase activity was detected within the vacuoles. The vacuoles induced by H pylori supernatant were then compared with vacuoles induced by trimethylamine, a weak base known to induce lysosomal swelling. Neutral red dye rapidly entered the vacuoles induced by either H pylori supernatant or trimethylamine, and both types of vacuoles were reversible. Compared with trimethylamine-induced vacuoles, the vacuoles induced by H pylori supernatant were larger and typically lacked a limiting membrane. In the early stages of formation, vacuoles induced by trimethylamine were labeled by lucifer yellow, a pinocytotic marker, whereas H pylori cytotoxin-induced vacuoles were not. These data suggest that trimethylamine-induced vacuoles arise directly from endocytic compartments, whereas H pylori cytotoxin induces vacuole formation via an autophagic mechanism.