Background: Etiology of inflammatory bowel diseases, chronic diseases of gastrointestinal tract, encompassing Crohn’s disease (CD) and ulcerative colitis (UC) remains unclear. It has been speculated that they are the result of an activation of the immune response to an unknown antigen. Microorganisms of the genus Helicobacter could be this unknown antigen. The aim of this study was to determine the presence of Helicobacter species in patients with IBD. Methods: The study was performed on 62 colon biopsies and serum samples taken from 30 patients with CD and from 32 patients with UC. 16S rRNA gene of Helicobacter spp. was amplified by PCR and analyzed by sequencing analysis. AntiH. pylori IgG antibodies detection was performed by ELISA. Results: In analyzed colon biopsies 25 (40%) were positive for Helicobacter 16S rRNA gene. H. pylori was detected in 16 (25%) patients whereas other Helicobacter spp. in 9 (15%) patients. In patients with CD H. pylori genetic material was detected in 5 biopsies whereas in patients with UC in 11 patients. Other Helicobacter species were detected in 3 patients with CD and in 6 patients with UC. Anti-H. pylori IgG antibodies were detected in 15 (50%) of samples from patients with CD and 15 (46%) of patients with UC. Conclusions: Results of our study suggest that microorganisms of the genus Helicobacter spp. might be involved in the pathogenesis of inflammatory bowel disease. Further studies are needed to establish the relationship between the presence of Helicobacter spp. and IBD.