Objective Carotid intima-media thickness (IMT) is used to assess cardiovascular risk and progression of atherosclerosis. It is known that regular physical activity of moderate intensity has beneficial effects on the vasculature. However, it is still discussed controversially whether prolonged exercise, including participation in exhaustive competitive sports such as long-distance races, has also beneficial effects or might even be harmful regarding the cardiovascular system. Patients and methods Thirty-eight male marathon runners (45.8 ± 7.3 years) were investigated twice (2009 and 2013) for their carotid IMT (using ultrasound techniques), anthropometrics and clinical chemistry. Additionally, training volume (running kilometres per year) and competition participation (half marathon, marathon and ultramarathon) within this follow-up period were assessed. Results During 3.8 ± 0.4 years of follow-up, runners performed 1587 (850-2500) training kilometres per year and participated in a total of 7 (4-12) long distance competitions. IMT increased in total by 0.05 ± 0.09 mm or annually by 0.013 ± 0.023 mm, respectively. Higher increase in IMT over that period was associated with higher fasting blood glucose (beta = .355, p = .045) at baseline examination. Effects of training volume and number of competitions on the progression of IMT could not be demonstrated in our longitudinal analysis. Conclusions Higher blood glucose levels are associated with detrimental effects on vasculature in otherwise healthy male marathon runners. Regular marathon training, including competition participation over at least several years, was not associated with detrimental effects on IMT or, vice versa, seems not to provide beneficial effects on vasculature.