We tested the utility of quantitative susceptibility mapping (QSM) to assess vascular abnormalities in a mouse model of experimental stroke. We acquired high resolution gradient echo data of mice at different time points after ischemia/reperfusion for computation of susceptibility maps. Prominent vessels with increased magnetic susceptibility values were detected surrounding the ischemic lesion at all times, indicating an increase in oxygen extraction. Immunohistochemistry revealed narrowed capillaries and dilated larger vessels. Thus, prominent vessels are an important indicator of underlying microvascular pathology and may by pivotal for diagnosis and therapeutic decision making in stroke patients.