Background Obstructive sleep apnea syndrome (OSAS), characterized by intermittent hypoxia/reoxygenation (IHR),has been identified as an independent risk factor for cardiovascular diseases (CVD). The CVD biomarkers associated with OSAS have not been thoroughly investigated.Methods Fifty-one men with OSAS recently diagnosed by polysomnography were classified into two groups according to the severity of apnea: moderate to severe OSAS group (n= 28) and mild OSAS group (n= 23). Twenty-five obese men,of comparable age and body mass index (BMI), without OSAS were chosen as control subjects. Serum metabolic variables, C-reactive protein (CRP) and matrix metalloproteinase-9 (MMP-9) were measured. Spearman correlation and regression analysis were performed.Results Serum concentrations of CRP and MMP-9 were significantly higher in 51 OSAS patients than in 25 control subjects. Levels of CRP and MMP-9 were significantly higher in patients with moderate to severe OSAS than in patients with mild OSAS or in obese control subjects. A positive correlation was found between levels of CRP and MMP-9 in OSAS patients. Regression analysis showed that after adjusting for age and BMI, apnea/hypopnea index (AHI) significantly correlated with serum concentrations of CRP and MMP-9 in patients with OSAS.Conclusions AHI, mirroring the frequency of IHR, was a predictor of enhanced circulating CVD biomarkers MMP-9 and CRP. Our data support the theory that IHR contributes to the upregulation of the inflammatory factors in OSAS patients.