BACKGROUND The main objective of this study was to investigate the correlation between the level of mucociliary dysfunction and severity of obstructive sleep apnea syndrome (OSAS). The effect of smoking in OSAS patients on mucociliary dysfunction was also assessed. METHODS It is a descriptive study that compares variables between groups (univariate analysis). In this clinical trial 122 patients with varying degrees of OSAS and 49 healthy volunteers were included (n = 171). Patients were divided into three groups as having mild, moderate, and severe OSAS, according to their apnea hypopnea index (AHI) values. (AHI values are typically categorized as 5-15/hr, mild OSAS; 15-30/hr, moderate OSAS; and >30/hr, severe OSAS.) The control group was comprised of healthy subjects. Each group was divided into smoking and nonsmoking subgroups. The mucociliary rates of the subjects were measured using the saccharin test. Statistical analysis was performed with the GraphPad Prism Version 3 pocket program. RESULTS Mild and moderate OSAS groups showed similar results with control group (p = 0.869), but severe OSAS patients showed a statistically significant difference with control group (Kruskal-Wallis [KW] = 32.28; p = 0.0032 and p < 0.05). Although in the moderate OSAS group the mucociliary clearance rates showed a tendency to decrease, this decrease was not significant (p = 0.453). A statistically significant difference was observed between smokers and nonsmokers in terms of mucociliary clearance times in all groups (KW = 18.24; p = 0.001). CONCLUSIONS The nasal mucociliary system is significantly deteriorated in severe OSAS patients and they should be meticulously observed to prevent sinonasal infections. Measures to enhance mucociliary activity in these patients should be taken. Smoking, a well-known inhibitor of mucociliary activity, also has a negative impact on the mucociliary function of OSAS patients and quitting smoking would be of benefit for these patients.