The aim of the PHD study was to characterize the pathogenicity of bacteria H. pylori and Candida fungi strains and to assess the co-existence of selected disorders of the upper gastrointestinal tract with infection of H. pylori and/or Candida spp. Two hundred and sixty seven dyspeptic patients undergoing upper gastrointestinal endoscopy were enrolled in the study. From each patient biopsy specimens of gastric mucosa were taken for histopathology, a rapid urease test and microbiological examination. H. pylori strains were isolated from 41% of patients whereas Candida fungi were found in 19% of patients, but in non-significant concentration, < 103 CFU/ml. It was proved that patients infected with cagA+, vacA s1 H. pylori strains are at a higher risk for peptic ulcer disease than those carrying cagA-, vacA s2 strains. Resistance to metronidazole, clarithromycin and to both metronidazole and clarithromycin was detected in 40%, 23% and 12% of H. pylori isolates, respectively, whereas 5% of strains were resistant to levofloxacin. It is noteworthy that two patients (2.5%) were infected with multidrug resistant H. pylori strains. Obtained data suggest that empirical eradication therapy should be replaced with the pretreatment susceptibility testing to improve the effectiveness of therapeutic treatment and to avoid increasing H. pylori drug resistance. The presence of Candida fungi in n ; on-significant concentration in patients with gastric ulcers infected with H. pylori and noninfected, probably was not associated with the pathogenesis of the disease but resulted from an earlier injury of gastric mucosa under the influence of H. pylori and/or other factors.