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Introduction Radiotherapy (RT) and some chemotherapy regimens are known risk factors predisposing to the development of premature arterial disease. Vascular ultrasound measurement of carotid intima-media thickness (IMT) is a non-invasive technique, useful to detect early subclinical symptoms of atherosclerosis that can appear in the paediatric population. We analysed the influence of chemotherapy and moderate doses of head or neck irradiation in childhood cancer survivors on the possibility of premature carotid artery disease. Methods Ultrasound measurements of the intima-media thickness (IMT) in the common carotid artery (CCA), bulb and internal carotid artery (ICA) were performed in 74 young cancer survivors and in 48 age- and sex-matched controls. Results In the whole study group, we observed higher IMT in all positions as compared with the control, except for comparable thickness in the CCA (bilaterally). We failed to find any differences in IMT between irradiated and non-irradiated females. In irradiated males, all IMT measurements on the right side were higher than in non-irradiated patients. There was no effect of body mass index, blood pressure, serum cholesterol, triglycerides, fibrinogen and thyroid hormones on IMT. In the irradiated group, a positive correlation was observed between IMT in the right bulb and the post-radiation time. Conclusions Anticancer treatment during childhood, especially including irradiation to the mediastinum, head or neck, affects the IMT, particularly in males. This suggests a possible role of irradiation in the premature development of carotid artery disease.