An investigation was conducted into whether running a marathon causes acute alterations in menisci, cartilage, bone marrow, ligaments, or joint effusions, which could be evaluated by magnetic resonance imaging (MRI). Twenty-two non-professional marathon runners underwent MRI of the knee before and immediately after running a marathon. Lesions of menisci and cartilage (five-point scale), bone marrow, ligaments (three-point scale), joint effusion, and additional findings were evaluated and a total score was assessed. Before the marathon, grade 1 lesions of the menisci were found in eight runners, and grade 2 lesions in five runners. After the marathon, an upgrading from a meniscal lesion grade 1 to grade 2 was observed in one runner. Before the marathon, grade 1 cartilage lesions were found in three runners, and grade 2 lesions in one runner, all of which remained unchanged after the marathon. Before and after the marathon, unchanged bone marrow edema was present in three runners and unchanged anterior cruciate ligament lesions (grade 1) were seen in two runners. Joint effusions were present in 13 runners in the pre-run scans, slightly increased in four runners after the marathon, and newly occurred in one runner after the marathon. A total score comprising all knee lesions in each runner showed an increase after the marathon in two runners, whereas no runner showed an improvement of the radiological findings (Wilcoxon signed-rank test, P>0.05). The evaluation of lesions of the knee with MRI shows that marathon running does not cause severe, acute lesions of cartilage, ligaments, or bone marrow of the knee in well-trained runners. Only subtle changes, such as joint effusions or increased intrameniscal signal alterations, were imaged after running a marathon.