Background: Intravascular thrombi change in time due to retraction and organization, which is reflected in the appearance of magnetic resonance images of clots. We have hypothesized that MRI has the potential to improve patient selection for thrombolytic treatment. The aim of our study was to analyze occlusive arterial thrombi with MRI, and to correlate the MRI parameters with the therapeutic outcome in patients with occlusive atherothrombotic disease of the superficial femoral artery who were treated with catheter-directed thrombolysis by streptokinase. Patients and methods: We included 13 patients with subacute (2 weeks to 3 months old) occlusive arterial thrombi and 4 patients with chronic (more than 6 months old) arterial occlusions. We measured the MRI signal intensity on gradient echo images of 98 axial slices of the subacute occlusive thrombi and in 45 slices of 4 chronic thrombi. Following MRI, the patients with subacute history were treated with catheter-directed thrombolysis. Results: Thrombolysis was successful in 11/13 patients. The normalized MRI signal intensity was significantly higher in the unsuccessfully treated thrombi than in the successfully treated thrombi (1.10 ± 0.08 vs. 0.72 ± 0.17, p < 0.003), but the subacute and chronic thrombi did not differ in signal intensity. Conclusions: High signal intensity of arterial thrombi on gradient echo MRI might predict resistance to thrombolytic therapy.