Helicobacter pylori since Marshall and Warren's discovery has been an object of interest of gastroenterologists and many researchers of other specialties. What needs to be highlighted is also the growing interest of dentists in the role of oral residue of H. pylori in oral pathologies such as burning mouth syndrome, periodontitis and gingivitis. With the development of medical techniques more studies using highly specific diagnostic methods are performed in order to determine the transmission pattern of bacterial infection. Suggested faecal-oral and oral-oral routes of bacterial transmission raised interest in molecular biology methods as tools for the study of these environments. Additionally, co-existence of helical and coccoidal forms of H. pylori in the mentioned niches raised the question whether the latter is potentially pathogenic. This is why molecular biology is now giving a great opportunity to explore parts of the human body that could not have been diagnosed before using only gold standard diagnostic methods. Molecular techniques have shown their usefulness in examining the potential virulence of coccoid forms of bacterium. This review was created also to summarize the knowledge about molecular methods, especially different PCR techniques, as diagnostic tools that can help medical teams during regular diagnosis of gastritis.