We conducted a case-control study in 62 participants, including 31 patients with severe AA (SALT > 75) and 31 healthy controls, matched for age, sex and body mass index (BMI). The participants underwent a detailed history assessment and were subjected to the measurement of weight, height, abdominal circumference and blood pressure. A fasting blood sample was also collected. Subclinical atherosclerosis was evaluated by ultrasonography of the bilateral femoral and carotid arteries. The AA patients had an increased prevalence of subclinical atherosclerosis (54.7%) compared to the healthy controls (22.6%, p = 0.010). The prevalence of atheroma plaques was significantly higher in the carotid arteries (41.90% vs. 12.9%, p = 0.009), while no significant differences were found in femoral plaque prevalence. The AA patients with atherosclerotic plaques were older (p < 0.001) and had a longer time since AA diagnosis (p = 0.11) and increased serum levels of glycated hemoglobin (p = 0.029) and triglycerides (p = 0.009). In a regression analysis, duration of disease and neutrophil/lymphocyte ratio were the main predictors of atherosclerosis. AA patients have an increased prevalence of carotid subclinical atherosclerosis. The duration of AA, systemic inflammation and insulin resistance appear to play a role in the development of subclinical atherosclerosis in this population.