Obstructive sleep apnea/hypopnea syndrome (OSAHS) is strongly associated with the increase of cardiovascular and cerebrovascular disorders. Carotid intima-media thickness (IMT) is used as a surrogate marker for subclinical or early atherosclerosis. Knowledge regarding early atherosclerosis in patients with OSAHS is scarce, and factors predicting carotid IMT have not been well studied. To compare IMT in patients with OSAHS versus controls and explore the factors associated with increased IMT in OSAHS. One hundred fifty-six OSAHS patients and 35 controls without history of vascular events, hypertension, and diabetes mellitus who underwent polysomnography were consecutively enrolled. Carotid IMT was measured using B-mode ultrasonography. Body mass index, waist circumference, hip circumference, waist-to-hip circumference ratio, Epworth Sleepiness Scale, and polysomnographic variables including arousal index, apnea/hypopnea index, mean oxygen saturation, and lowest oxygen saturation were assessed. Fasting plasma glucose, blood lipid profile, and high-sensitivity C-reactive protein were measured. Average carotid IMT of OSAHS patients was significantly thicker than controls (0.66 vs. 0.58 mm, P=0.002) and multivariable logistic regression analysis revealed that arousal index [odds ratio (OR), 0.77; confidence interval (CI), 0.63-0.95; P=0.01] and lowest oxygen saturation (OR, 1.91; CI, 1.24-2.95; P=0.003) were significantly associated with OSAHS patients. Among the OSAHS patients, age (OR, 1.16; CI, 1.10-1.22; P<0.0001), fasting plasma glucose (OR, 1.05; CI, 1.01-1.10; P=0.04), low-density lipoprotein cholesterol (OR, 1.03; CI, 1.02-1.05; P<0.0001), and high-sensitivity C-reactive protein (OR, 1.48; CI, 1.13-1.95; P=0.005) were significantly associated with patients with IMT≥0.65 mm. IMT was thicker in OSAHS patients without history of vascular events, hypertension, and diabetes mellitus. This study demonstrates that early atherosclerosis exists in this group of patients.