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104 patients with the inflammatory diseases of stomach and duodenum were investigated. Levels of the IL-1β, IL-2, IFN-γ in blood serum were detected by ELISA. For detection of Helicobacter pylori (H. pylori) and Herpes viridae in biopsies from the zone of inflammation polymerase chain reaction (PCR) was used. Expression of mRNA cytokines: Il-1β, Il-2, Il-4, Il-6, Il-10, Il-18, IFN-γ, TNF-α in biopsies from 37 patients was detected by real time PCR. Results of biopsies revealed high frequency of detection of pathogenic strains of H. pylori (80%) and Herpes viridae (EBV, HHV-6, HHV-7, HHV-8) in various combinations. The increased levels of IL-1β, IL-2, IFN-γ in serum and of mRNA cytokines in infected mucous membrane were observed.