In humans, Helicobacter pylori and some other members of Helicobacteraceae are known to be implicated in both inflammatory and non-inflammatory gastrointestinal disorders. So far, conclusive evidence regarding the potential involvement of helicobacters in development of chronic inflammatory lesions of canine stomach and intestine is missing. The aim of the study was to determine the prevalence of Helicobacter-like organisms in endoscopic biopsy samples of different parts of the gastrointestinal tract of dogs with chronic inflammation and to reveal their potential relationship to the presence and severity of morphological and inflammatory changes. A total of 183 samples of inflammatory lesions were examined histologically and immunohistochemically. Helicobacter-like organisms were found in 64.1% of samples of gastritis, 5.3% of cases of duodenitis, 47.6% of cases of ileitis and 48% of cases of colitis. The most frequent gastric morphological change was surface epithelial injury. In duodenum epithelial injury together with villous stunting, and in ileum villous stunting were the most commonly observed morphological changes. Crypt dilation/ distortion was the most frequent morphological abnormality among colonic samples and was significantly more often a feature of colitis than duodenitis and ileitis. Our data show no effect of colonization with Helicobacter-like organisms on the presence of gastric pit epithelial injury and gastric mucosal fibrosis. No association was found between the presence/density of Helicobacter-like organisms and the presence or severity of morphological and inflammatory lesions of duodenal, ileal, and colonic mucosa.