Chronic rhinosinusitis is a symptomatic inflammation of the mucosa of the nose and paranasal sinuses lasting for at least 12 weeks. Atypical bacteria Chlamydophila pneumoniae and Mycoplasma pneumoniae are important causes of human respiratory tract infection. Also, they were identified in bronchial respiratory epithelium of patients with chronic obstructive pulmonary disease or asthma. Having in mind the unified airway concept, it is also possible that these bacteria can cause persistent infection of sinus mucosa in patients with chronic rhinosinusitis. Sixty consecutive patients with chronic rhinosinusitis who underwent the functional endoscopic sinus surgery due to medical therapy failure were included in the study. During the operation, sinuses were irrigated with sterile 0.9% NaCl solution and this lavage was immediately aspirated. Aspirates were used for the detection of C. pneumoniae and M. pneumoniae DNA using real-time PCR. C. pneumoniae and M. pneumoniae DNA were not detected in samples analysed. Atypical bacteria C. pneumoniae and M. pneumoniae did not cause persistent infection of sinus mucosa in patients with chronic rhinosinusitis.