Aortic dissection is a life-threatening cardiovascular disease with high in-hospital mortality. However, the risk factors of aortic dissection have not been fully elucidated. Obstructive sleep apnea (OSA) has been increasingly recognized as an independent cardiovascular risk factor. Among the underlying mechanisms to explain the association between OSA and cardiovascular morbidity, previous studies reported that intermittent hypoxia and re-oxygenation (IHR) might induce cardiovascular diseases via atherosclerosis. However, little is known about an association between aortic dissection and IHR. The aims of the study were to investigate the prevalence of nocturnal IHR among patients with aortic dissection and compared with that in subjects without aortic dissection, and to investigate whether there is an independent association between aortic dissection and IHR. We enrolled 29 patients with aortic dissection and 59 control subjects. We performed sleep studies and compared the results between the groups. Frequency of IHR is expressed as 3% oxygen desaturation index (ODI). Multivariate analysis was performed to identify determinants of aortic dissection. The percentage of either moderate-to-severe IHR or severe IHR was significantly higher in the aortic dissection group (p = 0.04 and <0.001, respectively) than in the control group. The mean 3% ODI of patients with aortic dissection was significantly higher than that of control subjects (34.8 ± 23.1 and 19.0 ± 14.1, p = 0.003). In multivariate analysis, 3% ODI was significantly associated with aortic dissection (odds ratio 1.44; 95% confidence interval 1.08-1.91; p = 0.01). The present study showed the close association between aortic dissection and, IHR, a major component of OSA.