Helicobacter pylori is a gram-negative bacterium associated with the development of severe gastric pathologies, such as atrophy, metaplasia, and gastric adenocarcinoma. This microorganism is considered a class I carcinogen by the International Agency for Research on Cancer. The virulence genes in the strain causing infection influence the clinical outcome and can be used as specific markers for the severity of gastric diseases. We evaluated H. pylori infection and associations of cagA, vacA and dupA virulence genes with gastric pathologies. Antral and gastric body biopsies of 117 patients with dyspepsia were analyzed by histological and molecular techniques. Screening for H. pylori infection was ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 20 (3): gmr18883 L.L.L. Silva et al. 2performed using the hpx gene (16S rRNA). Positive samples were evaluated for vacA, cagA, and dupA virulence genes. The clinical outcomes presented by the patients were stratified according to severity, being considered severe lesions atrophy, metaplasia and adenocarcinoma. Gastritis, duodenitis, esophagitis, ulcer, and xanthelasma were considered non-severe pathologies. The prevalence of infection was 64.1%, with a high frequency of strains positive for cagA (80.0%), dupA (70.7%), and vacA (56.0%). The cagA gene was detected in all isolates from patients with severe pathologies, whereas the vacA gene was not detected in this group. Simultaneous detection of the three genes was observed in 14.3% and 35.8% of the isolates from individuals with severe and non-severe pathologies, respectively. Furthermore, fewer virulence genes were detected in isolates from patients with severe disease (0.7) than in isolates from non-severe cases (1.4). Patients with severe diseases had a higher mean age and greater number of gastric diseases than patients with non-severe pathologies. The circulating H. pylori strains in the Brazilian Midwest exhibit high heterogeneity in the frequencies of virulence genes. Individual virulence factors and their combinations may influence clinical outcomes.