Abstract: OBJECTIVE To explore the clinical effect and significance of pathological diagnosis of Helicobacter pylori and fungal infections in patients with gastric diseases so as to improve the clinical diagnosis of gastric diseases such as gastric ulcer and gastric cancer and provide guidance for the treatment. METHODS A total of 300 patients with gastric diseases who were treated in the hospital from Jan 2015 to Sep 2015 were enrolled in the study and divided into the gastric cancer group with 120 cases and the gastric ulcer group with 180 cases according to the type of disease. The gastric mucosal tissue specimens were collected by using gastroscope and treated with routine paraffin sections and HE and Giemsa staining. The isolation rates of H.pylori and fungi were observed and compared between the two groups of patients, and the statistical analysis of data was performed with the use of SPSS18.0 software. RESULTS The isolation rates of H.pylori and H.pylori mixed with fungi were respectively 68.3% and 50.8% in the 120 gastric cancer patients, significantly higher than 60.6% and 34.4% in the gastric ulcer patients (P<0.05). The isolation rate of fungi of the gastric cancer patients was 35.0%, significantly lower than 56.1% of the gastric ulcer patients (P<0.05). Among the 300 patients with gastric diseases, the H.pylori strains were blue under the HE staining, each single strain showed short rod; while the fungi were characterized by big wave shape under the HE staining. The H.pylori strains showed purple under the Giemsa staining, and the fungi showed clear distribution under the Giemsa staining. CONCLUSION The incidence rates of H.pylori and fungal infections are simultaneously high in the patients with clinical diagnosis of gastric diseases, and it is necessary to conduct the appropriate treatment on the basis of detection results.