The Syndrome of obstructive sleep apnoea (OSA) is associated with an increased risk of arterial hypertension, metabolic syndrome, diabetes mellitus type 2, brain-vascular damages and atherosclerosis. The aim of this study is to assess the connection between iron metabolism dysregulation in OSA and atherosclerotic changes of carotid arteries. Thirty-five OSA patients with brain-vascular atherosclerotic evidences were included in this study; changes were evaluated by carotid artery intima-media thickness (IMT) and flow-mediated dilatation (FMD). Their results were compared to an equal number of healthy volunteers. Haematological and biochemical assays were performed in all participants in the study. Serum hepcidin levels are statistically significantly increased in OSA patients with atherosclerotic a. carotis changes (101.9±10.1 µg/L) compared to the control group (18.5±2.5 µg/L); $$P<0.001$$. Serum homocysteine levels are significantly higher in OSA than in healthy people. Average IMT (1.22±0.19) and ABI (1.71±0.14) values in OSA patients with atherosclerotic a. carotis changes are increased in comparison to the control group (0.34±0.07, 1.11±0.06, resp.); $$P<0.001$$. Serum vitamin B12 levels were lower in OSA patients with atherosclerotic changes in carotid arteries (71.7±9.9 pmol/L) compared to the controls (449.7±21.4 pmol/L); $$P<0.001$$. A connection between iron homeostasis and atherosclerotic changes was established during this study. Increased hepcidin and homocysteine concentrations might be connected to an elevated risk of cardio- and brain-vascular diseases in OSA. The use of these markers in the routine practice may be very useful for early atherosclerosis assessment in OSA.