Helicobacter pylori has been recently detected in the oral cavity and oropharynx. However, the role it plays in oral and oropharyngeal pathogenesis remains unclear. The virulence of H. pylori strains can be distinguished according to the virulence factors genes carried. Our research has been focused on realtime PCR analysis of cagA and vacA genes of H. pylori strains in tonsils and tonsillar squamous cell cancer and their comparison with H. pylori strains obtained from the gastric mucosa of the same patients. Urea breath test (UBT) test was used to detect a gastric H. pylori infection in 20 patients with previously proven H. pylori in the oropharynx. Genotyping of H. pylori in gastric biopsies was performed in patients with positive gastric infection. Out of 20 patients positive for oropharyngeal H. pylori, 8 were positive for concurrent gastric H. pylori infection. In 6 of them gastric biopsies were obtained. Comparison of oropharyngeal and stomach H. pylori genotypes showed important differences. Four of 6 patients had different H. pylori strains in the oropharynx and stomach. The differences were found in cagA gene as well as in vacA gene. The finding of oral presence of H. pylori without concurrent stomach infection was confirmed using UBT. The results show that more than one H. pylori strain can be present in oropharynx and stomach in the same patient. The oropharyngeal infection seems to be independent to the gastric infection.