Objective: To investigate the expressions of serum inflammatory markers and markers for endothelial function in patients with sleep apnea syndrome (SAS) complicated with stroke, and explore the risk factors related to stroke onset in SAS patients. Methods: This study included 35 patients with simple SAS and 38 SAS patients complicated with stroke. The expression levels of serum endothelial nitric oxide synthase, malondialdehyde (MDA) and tumor necrosis factor α (TNFα) were detected and compared between the simple SAS patients and the SAS patients complicated with stroke. The related factors of stroke onset in patients with SAS were examined. Results: The expression levels of serum endothelial nitric oxide synthase, MDA and TNFα in SAS patients complicated with stroke were significantly higher than those in simple SAS patients (all P = 0.000). Univariate analysis showed that gender (P = 0.012), age (P = 0.009), the course of SAS (P = 0.000) and the history of hypertension (P = 0.000) were associated with stroke onset in SAS patients. Multivariate analysis showed that the course of SAS [hazard ratio: 9.12 (95% confidence interval: 2.15-13.88); P = 0.000] and the history of hypertension [hazard ratio: 5.05 (95% confidence interval: 2.74-10.52); P = 0.000] were the independent factors for stroke onset in SAS patients. Conclusion: The expression levels of serum inflammatory markers and markers for endothelial function in SAS patients complicated with stroke are increased, indicating the further dysfunction of endothelial cells. The course of SAS more than one year and the history of hypertension are independent risk factors involved in the onset of stroke in SAS patients.