Sleep apnea syndrome (SAS) is basically divided into two types: obstructive and central SAS. Recently, the concept of complex SAS has been advocated. Complex SAS is defined as SAS that initially manifests as primarily obstructive SAS, but is characterized by the frequent central apneas after the removal of upper airway obstruction. To determine the prevalence and clinical significance of complex SAS among Japanese patients with SAS, 1,312 patients with SAS were enrolled in this study. Diagnosis of central SAS was made based on diagnostic polysomnography, and differentiation of obstructive SAS from complex SAS was made from polysomnographic findings for treatment with continuous positive airway pressure, which resolved upper airway obstruction. As a result, obstructive SAS was found in 1,232 of 1,312 patients with SAS (93.9%) and central SAS was found in 14 patients (1.1%). The overall prevalence of complex SAS was 5.0% (n = 66). The prevalence of complex SAS among 1,218 male and 94 female patients with SAS were 5.3% and 1.1%, respectively. Patients with complex SAS had significantly higher apnea/hypopnea indices than patients with either obstructive or central SAS, but were similar in both mean age and average body mass index to obstructive SAS patients. There were no significant between-group differences in numbers of patients with clinical complications including hypertension, cardiac diseases, or cerebrovascular diseases. In conclusion, the prevalence of complex SAS in Japanese SAS patients is 5.0%, which is lower than previously reported prevalence of complex SAS in the USA and Australia.