Several studies report neurological complications such as brain injury induced by ischemia or edema following exhaustive endurance sport. We aimed to detect the frequency of acute brain lesions after a marathon race. In the prospective observational Berlin Beat of Running study, 110 experienced endurance athletes underwent 3-Tesla brain MRI exams 2-3 days prior and within 2 days after a marathon run. MRI results were compared to an age- and sex-matched control group of 68 non-athletes, including the "Age-Related White Matter Changes" (ARWMC) scale to assess white matter lesions (WML) in the brain. 108 athletes (median age 48 years, 24% female, 8% with hypertension; 0% with diabetes) completed the race. No athlete reported neurological deficits, but a single acute ischemic lesion was detected in diffusion-weighted MRI after the race in one athlete. No other acute brain lesions compared to prior MRI were found. An ARWMC score ≥4 was found in 15% of athletes and 12% of non-athletic controls (p=0.7). Chronic ischemic lesions were not found in athletes but in four controls (6%) (p=0.02). In conclusion, acute ischemic brain lesions may be found in endurance runners. Every seventh endurance athlete and every ninth control showed evidence for substantial white matter lesions.