Background: The role played by Helicobacter pylori in the sinuses, and its association with the same organism's gastric infection, are still unclear. Methods: In order to compare H.pylori colonization patterns in the nose and stomach we conducted a cohort analysis of 14 patients, eligible for sinus surgery due to chronic medically refractory rhinosinusitis, who were tested for simultaneous presence of H. pylori, by histology, culture and polymerase chain reaction, in pathologic sinus tissue collected during surgery and in gastric mucosa obtained through gastroduodenal endoscopy. Results: H. pylori DNA was found in the sinus mucosa of 15.4% of patients with chronic rhinosinusitis, and all of them showed concurrent H. pylori stomach infection. Sinus colonization was not found without simultaneous gastric colonization, although most patients with gastric infection did not have the bacterial DNA in their sinuses. H. pylori's presence in the nose was not associated with local inflammatory status, and no cultures could be obtained from any of the sinus tissue samples, including those positive for H. pylori DNA. Conclusions: Only H. pylori DNA, and not the culturable active form of the microorganism, could be found in the sinus mucosa of some patients with H. pylori gastric infection. We could not find evidence, however, that the bacterium's presence in the nose contributes to local mucosal inflammation.