To investigate the pathophysiological mechanisms underlying the effects of obstructive sleep apnea syndrome (OSAS) on olfactory functions.Study subjects consisted of patients with newly diagnosed OSAS divided by polysomnography into subgroups of mild, moderate, and severe disease. Subjects identified as not having OSAS served as controls. All subjects were subjected to the Sniffin' Sticks test to evaluate olfactory functions. Control subjects and subgroups with OSAS were compared for sleep characteristics and olfactory scores. In the patient group, correlations were investigated between olfactory scores and polysomnographic parameters.Of 99 subjects (64 men), there were 20 controls, 23 with mild OSAS, 25 moderate, and 31 severe. There was a decreasing trend from the control group towards the severe subgroup in mean odor threshold, odor discrimination, odor identification, and threshold-discriminationidentification (TDI) scores. In the patient group, there was a strong inverse correlation between AHI and TDI scores (r = - 0.62, p < 0.001). Arousal index and TDI scores had a strong negative correlation (r = - 0.81, p < 0.001). There was a weak positive correlation between the minimum SPO2% and TDI scores (r = 0.34, p = 0.002) and a weak negative correlation between TST <90% and TDI scores (r = - 0.24, p = 0.027).The finding that arousal index showed a stronger correlation with odor scores than with hypoxemia-related parameters suggests that sleep fragmentation may be a more prominent mechanism underlying the pathophysiology of olfactory malfunction in patients with OSAS.