Objectives: Among different theories about pathogenesis of obstructive sleep apnea syndrome (OSAS), dysfunction of upper airway muscles still awaits to be delineated. The aim of this study is to examine differences in motor unit potential (MUP) parameters of upper airway muscles between OSAS patients and healthy controls. Methods: Ten male patients diagnosed as OSAS by whole-night polysomnography were analyzed for MUP parameters of genioglossus (GG) muscle, palatoglossus muscle (PG), palatopharyngeus muscle, and uvular (U) muscle. Eight healthy volunteer men matched by age were enrolled as a control group. Results: In PG muscle parameters, the mean MUP area was significantly smaller (P = 0.040) in OSAS patients than those in controls. On the other hand, U muscle parameters showed a significantly larger mean MUP area (P = 0.022) in OUAS patients compared to those in the control group. In OSAS patients, the percentages of polyphasic MUPs of GG and PG muscles were significantly high (P < 0.001 and P = 0.05, respectively). Body mass index was positively correlated with number of phases of GG muscle (rs = 0.63, P < 0.05) and duration of U muscle (rs = 0.71, P < 0.05) in OSAS patients. Other MUP parameters of palatal muscles were similar between the two groups. Conclusion: Our results showed that, although mild in severity, structural neurogenic and myogenic changes characterized as mild and nonuniform MUP changes may co-exist in OSAS patients. These changes in palatal muscles may be attributed to compensatory adaptation of muscle fibers to other precipitating factors in OSAS.