To observe the effect of Helicobacter pylori(H. pylori) on cell gap junction ultrastructure of gastric epithelial cells, and to explore carcinogenic mechanism of H. pylori from the changes of cell gap junction, BGC-823 cells were co-cultured with different H. pylori strains for 24 h and 48 h. The cell gap junction ultrastructure was observed under transmission electron microscope with sample preparation of fixation and embedding in situ. In 70 patients with gastric cancer(GC), H. pylori was detected by rapid urease test, basic fuchsin stain and ¹⁴C-urea breath test. The CagA gene of H. pylori was determined by PCR and the cell gap junction ultrastructure was observed under transmission electron microscope. More cell gap junctions and junction complexes of BGC-823 cells were found in control group without H. pylori. Groups with H. pylori had less number of cell gap junctions, less number of junctions/ unit perimeter, shorter length of junctions /unit perimeter, and bigger width of the intercellular space, comparing to control groups without H. pylori(P < 0.001 or P < 0.005). The number of cell junctions and the number of junctions/unit perimeter in the groups co-cultured with NCTC J99, GC 01 and NCTC 11639(CagA+) were less than that in the groups co-cultured with NCTC 12908(CagA^-) (P < 0.001 or P < 0.05), and the length of junctions/unit perimeter in the groups co-cultured with NCTC J99 and GC 01 was shorter than that in the groups co-cultured with NCTC 12908 (P < 0.001). In patients with GC, the number of cell junctions, the number of junctions/unit perimeter and the length of junctions/unit perimeter in group H. pylori infection were all less than those in group without H. pylori infection(P < 0.001), and that in CagA⁺ H. pylori group were less than that in CagA^- H. pylori group, but its smallest width of the intercellular space was longer than that in CagA^- H. pylori group. The above results showed that the changes of cell gap junction of gastric epithelial cells were associated with H. pylori infection especially CagA⁺ H. pylori infection.