Helicobacter species such as H. heilmannii, H. pylori, H. felis, H. bizzozeronii and H. salomonis have been identified in cats and dogs, and research suggesting that these species may be zoonotic agents and has been studied intensified in recent years. The aim of this study was to reveal the presence, comparing the histopathological findings and Real-time PCR results of H. felis, H. heilmannii, and H. pylori in the stomach and liver tissues taken during the necropsies of owned, stray or shelter dogs. The material of the study consisted of stomach and liver tissues taken from 35 dogs that died for different reasons and were brought for necropsy. DNA copies of H. heilmannii were detected by Real-time PCR in the liver samples of 30 dogs using H. heilmannii-specific primers. In the case of gastric samples, Realtime PCR detected H. heilmannii in 13 cases, H. pylori in 3 cases, both H. heilmannii and H. pylori in 13 cases, and H. felis, H. heilmannii and H. pylori in 3 cases. Microscopically, neutrophil leukocyte infiltration, epithelial degeneration, fibrosis and oedema in the lamina propia, and lymphoplasmacytic cell infiltration were determined in the stomachs. In the Hemotoxylin Eosin staining of the sections, 5 cases and 14 cases in the Warthin–Starry staining were found positive for Helicobacter-like microorganisms. Microscopically, dissociation of the remark cords and hydropic degeneration in hepatocytes, and focal mononuclear cell infiltrations in some sections were determined in the livers. In conclusion, with this study, it was understood that Real-time PCR analyzes are very useful in the diagnosis of H. felis, H. heilmannii, and H. pylori. However, histopathological examinations are necessary to associate the presence of bacteria with the development of the disease.