Endoscopic biopsies of antral mucosa from 26 patients with Helicobacter pylori-associated gastritis were studied by electron microscopy (EM). Scanning electron microscopy (SEM) showed clustering of H. pylori in the intercellular areas, being entrapped by the microvilli which were decreased at the sites where the bacilli were seen. The observations of SEM were confirmed by transmission electron microscopy (TEM), which showed adherence of the bacilli to the cell surface, producing cup-shaped depressions in the epithelial cells, and occasionally intracellular infiltration by H. pylori. There were also depletion of mucus granules, degenerative changes, and disruption of intercellular junction complexes of the epithelial cells. Post-treatment biopsies showed complete disappearance of the bacilli, and ultrastructural changes associated with H. pylori infection were resolved.