In familial hypercholesterolemia (FH) the level of LDL cholesterol is 2–3 times that of the normal population and leads to accelerated atherosclerosis. Improved care for risk factors has decreased cardiovascular mortality of these patients. We studied subclinical atherosclerotic changes with morphologic and functional aortic magnetic resonance imaging (MRI) in FH patients under the age of 50. 39 DNA test-verified heterozygous FH-North Karelia patients, aged 6–48, 28 of them treated with statins, and 25 healthy controls, aged 12 to 50, underwent aortic MRI, carotid ultrasound (US), and risk-factor assessment. No differences in any of the morphologic or functional aortic parameters appeared between patients and controls. Age and gender were independent predictors of the majority of the morphologic and functional measures. Carotid intima-media thickness assessed by US was greater in patients (0.57 mm ± 0.13 vs 0.48 ± 0.13 mm, p = 0.005) as was cholesterol-years score (243 ± 122 vs 137 ± 74, p < 0.001). Patients had thicker intima-media of the common carotid artery and higher cholesterol burden as indicated by their cholesterol-years score. Despite this, no differences existed in morphologic or functional aortic parameters assessed with MRI. The improved care of cardiovascular risk factors, especially statin treatment, may protect the aorta of FH patients. However, larger confirmatory studies are needed.