The diagnostic standard is an important factor in the evaluation of the antibacterial effect to Helicobacter pylori (H. pylori). Few studies have evaluated the bacterial morphological change. In the present study, H. pylori was examined by means of electron microscopy (EM), light microscopy (LM) and immunohistochemical staining. Patients were followed up from 6 weeks to more than 1 year after treatment for H. pylori, and the results of the 13C-urea breath test (UBT) were compared. A '4-L' evaluative system was used for histological diagnosis; that is, complete, significant, partial and negative response for H. pylori treatment. Complete response showed no H. pylori in histology, and positive 13C-UBT and negative response showed positive in both diagnoses. A significant response showed the morphology of H. pylori was thick walled by EM, that there was no obvious active inflammation, and was negative for C-UBT. These H. pylori showed a coccoid form and possibly static bacteria, which was resistant to further antibacterial therapy. The '4-L' system could evaluate the antibacterial effect, suggesting the necessity for a second line of therapy for H. pylori. It is suggested that this sensitive evaluative system is suitable for clinical applications for antibacterial therapy.