OSA and insomnia frequently co-occur. This is also called comorbid insomnia and sleep apnea (COMISA). Early recognition is important because both sleep disorders can adversely affect each other. However, the diagnosis of COMISA is still challenging. In this research, we investigated the differences in sleep structure between patients with pure OSA, pure insomnia and COMISA. The results show that the number and duration of wake periods can play a role in distinguishing OSA and COMISA. These variables could help improve the diagnosis of COMISA.