Compared with rhinologic patients without chronic rhinosinusitis (CRS), a higher prevalence of sinonasal Helicobacter pylori (HP) in patients with CRS was found. This study investigated if HP sinonasal colonization has a prognostic value for efficacy of functional endoscopic sinus surgery (FESS). Nasal polyps of 40 patients with CRS, undergoing FESS, were analyzed for presence of HP using immunohistochemistry (IHC). Patients were categorized as to whether the IHC was positive (HP+ group) or negative (HP- group). HP+ group and HP- group were compared according to the nasal polyp eosinophil density, and to the improvement (difference between pre- and post-operative scores) of the subjective symptom scores, and the nasal endoscopic scores. Nasal polyps in 28 (70%) patients were positive for HP. There were no significant differences between HP+ group and HP- group comparing the eosinophils, and the improvement of the single symptom and the total symptom scores. HP+ group had significantly greater improvement of the nasal endoscopic scores (F[1.38] = 6.212; P = 0.017). There is no influence of sinonasal HP on tissue eosinophilia and on CRS symptoms. There is a prognostic value for endonasal findings: CRS patients with HP have statistically significant greater improvement of the postoperative endoscopic scores.