The aim of the study was to demonstrate the effects of nasal CPAP treatment on the morphology and function of nasal mucosa in patients with obstructive sleep apnea (OSA). Patients with complaints relevant to OSA underwent respiratory function tests, arterial blood gas analyses and polysomnography. Saccharine test and nasal biopsies were performed to assess the mucociliary transport time and to observe the histopathological changes in patients with apnea-hypopnea index ≥15 in whole night polysomnography. Tissue samples were obtained from middle and inferior turbinates and septal mucosa to observe the degree of inflammation and fibrosis by semiquantitative means. Biopsies and mucociliary transport test were performed before and 3 months after the initiation of CPAP treatment. A total of 25 patients with a mean age of 52 were enrolled in the study. While the pretreatment mucociliary transport time before and 3 months after the treatment were 10.50 and 11.50 min respectively. The difference between these values was statistically insignificant. Mean apnea-hypopnea index was 63.19, while mean partial oxygen pressure was 75.46 mmHg. Nasal CPAP treatment was introduced with a mean pressure of 9.54 cmH2O. The degree of inflammation and fibrosis was found to be significantly increased after CPAP treatment. Nasal CPAP leads to alterations in mucosa. Efforts should be directed to make CPAP treatment a safer method via protecting the morphologic and functional properties of the nasal mucosa.