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The role of fungi in chronic rhinosinusitis (CRS) remains unknown. Fungi were also determined as one of the responsible agents in the etio-pathogenesis, while several studies found fungi in 6-93% of the cases. The aim of this study is to test the presence of fungi in samples taken from the middle meatus of patients with CRS, using traditional culture methods and polymerase chain reaction (PCR), and to compare the efficacy of these methods. Thirty patients diagnosed with CRS, with or without nasal polyposis, undergoing an operation in the Otorhinolaryngology Clinic, were prospectively included in the study. Nasal mucosa samples from ten patients, who were operated for pathologic evaluation, and without CRS, were used as controls. Nasal samples were taken from each patient by swabbing with a cytology brush. Middle meatus culture samples were taken by using nasal cotton swab, and the polyp and/or sinus mucosa samples were taken during endoscopic sinus surgery. Fungal specific PCR, using 18S rRNA primers and standard cultures, were performed on every sample. All amplicons were sequenced. There was no fungal growth in the Sabouraud dextrose agar (SDA) medium from middle meatus samples and tissue parts. Of 30 tissue and brush samples, 3 and 2 were positive for fungal DNA, respectively. Sequence analysis showed that four amplicons were homologus to Cladosporium herbarum and one to Aspergillus amstelodami. We concluded that fungal etiology is overestimated and fungi rarely play a role in patients with CRS. Large-scale studies should be done using molecular methods.