Presence of cagA gene of Helicobacter pylori (H. pylori) increases proliferation of stomach mucosa and it is an index of raised virulence of the bacteria. The vacA gene of H. pylori induces a serious inflammation of stomach. The purpose of this study was to determine cagA and vacA genotypes of H. pylori using real-time polymerase chain reaction (PCR) method with the double strain DNA-(dsDNA) binding SYBR Green I. dye. Results were compared with those of two immunohistochemical methods. 43 patients' paraffin embedded biopsy tissue samples were examined by histology, epidermal growth factor receptor (EGFR), proliferating cell nuclear antigen (PCNA) immunohistochemistry and melting curve analysis of real-time PCR using LightCycler instrument. Results of histology and real-time PCR from gastric biopsies correlated in 57% of cag acases and in 58% of vac cases. Significant difference was detected between normal and gastritis cases in the presence of cagA gene (p = 0.003) and between normal epithelial and intestinal metaplasia cases in the presence of vacA gene (p = 0.045) by investigation of association of histology and genotype of bacterium. Statistically significant difference (p = 0.02) was found between increased cell proliferation and the presence of gastritis. Significant correlation was found between the presence of cagA gene and EGFR expression in intestinal metaplasia cases (p = 0.0418). Results underlie the statistics that infection with cagA positive H. pylori strain increases the cell proliferation on the stomach mucosa and raises the chance of development of intestinal metaplasia. Infection with vacA positive H. pylori inhibits the signal-transduction pathway of EGFR, which influences mechanisms of mucosa repair. The role of EGFR and H. pylori infection is yet unclear in intestinal metaplasia and cancer. The authors' method seem to be suitable for determination of genotypes of H. pylori.