Helicobacter pylori (H. pylori) has been presumed to be an initiating factor in a previously recognized chain of events, starting with active chronic gastritis and leading to atrophy of the mucosal membrane, intestinal metaplasia, dysplasia (intraepithelial neoplasia), and finally culminating in gastric carcinoma. Adherence of H. pylori to the gastroduodenal epithelium is believed to be an important step in the induction of active chronic inflammation of the mucosal layer. However, it is not clear how the pathogen chronically colonizes the gastroduodenal epithelium. In this study, 30 biopsy specimens from H. pylori-positive peptic ulcer (15 for gastric ulcer, 15 for duodenal ulcer) patients were examined by transmission electron microscopy (TEM) to observe the structural adherence of H. pylori to gastroduodenal epithelium while ten healthy postulants were served as controls. We also investigated the interaction between H. pylori and gastroduodenal epithelial cells. Morphological appearances of both the pathogen and the cells as well as features of colonization, attachment, and internalization were observed. H. pylori exhibited both spiral and coccoid forms. Cytoplasmic vacuolar degeneration played by the vacuolating toxin (VacA) was apparent in gastroduodenal epithelial cells. Specially, a number of tumor cells were found in H. pylori-positive gastric intestinal metaplasia (IM) mucosa under TEM which provided an ultrastructural evidence of IM carrying a particularly high risk for the development of gastric cancer.