Data regarding cardiovascular risk in subjects with non-functioning adrenal adenoma are limited. The objectives of this study are to investigate carotid intima media thickness (IMT) as an indicator of atherosclerosis in subjects with non-functioning adrenal incidentaloma (AI) and to evaluate the factors that could be associated with IMT. Forty-nine subjects without findings of hypercortisolism or other adrenal gland disorders, 34 body mass index (BMI)-unmatched controls (C) and 18 BMI-matched controls (BC) were enrolled. Participants underwent hormonal evaluation including morning cortisol, adrenocorticotrophic hormone (ACTH), post dexamethasone suppression test cortisol (DST), dehydroepiandrosterone sulfate (DHEAS), and urinary free cortisol. Anthropometric and metabolic parameters and carotid IMT were measured. AI group had increased BMI, blood pressure, waist circumference, post DST cortisol, uric acid, and homeostasis model assessment (HOMA) levels when compared with C. Blood pressure, uric acid and, post DST cortisol remained significantly elevated in AI versus BC. Average IMT was increased significantly in AI versus C (0.74 mm vs. 0.68 mm, P = 0.029) and insignificantly elevated in AI versus BC (0.74 mm vs. 0.67 mm, P = 0.086). In all participants, IMT was correlated with age, BMI, HOMA, waist circumference, morning cortisol, and uric acid. Morning cortisol was independently associated with HOMA levels in both AI group and all participants. Increased IMT in non-functioning AI was a consequence of insulin resistant state associated with subtle cortisol autonomy rather than a direct effect of cortisol. The correlation between morning cortisol and IMT may be associated with the effect of hypothalamus-pituitary-adrenal axis disturbances on vasculature.