Lifestyle risk factors, inflammation and genetics play a role in the development of atherosclerosis. We therefore studied Fc gamma receptor (FcγR) polymorphisms, interleukin (IL)-10 polymorphisms and other biomarkers related to carotid intima-media thickness (cIMT) in patients with ischemic stroke at a young age. Patients were evaluated 12 years after stroke occurrence. Patients (n = 232) 49 years of age or younger with an index stroke between 1988 and 1997 were retrospectively selected. Blood samples were taken at a first follow-up 6 years after the stroke. At a second follow-up, additional arterial events were registered for 140 patients, new blood samples were taken, and measurements of cIMT and blood pressure (BP) were performed. Unadjusted logistic regression analysis showed that cIMT ≥1 mm was associated with age, male gender, additional arterial events, BP, cholesterol, sedimentation rate, haemoglobin, triglycerides, creatinine, glycolysed haemoglobin (HbA1c) and FcγRIIIB-NaII/NaII. Adjusted backward stepwise logistic regression showed significance for age (odds ratio (OR) 1.13, 95 % confidence interval (CI) 1.04 to1.23, p = 0.003), male gender (OR 4.07, 95 % CI 1.15 to 14.5, p = 0.030), HbA1c (OR 6.65, 95 % CI 1.21 to 36.5, p = 0.029) and FcγRIIIB-NaII/NaII (OR 3.94, 95 % CI 1.08 to 14.3, p = 0.037). In this long-term follow-up study of patients with ischemic stroke at a young age, FcγRIIIB-NaII/NaII was identified as a possible contributing factor for cIMT ≥1 mm together with known risk factors, such as age, male gender, systolic BP, additional arterial events and HbA1c.