Magnetic resonance imaging (MRI) is an important aid for physicians in the diagnosis and management of patients with acute ischemic stroke. Quantitative susceptibility mapping (QSM) has been recently introduced as a novel MRI post-processing technique of gradient recalled echo (GRE) data. QSM yields quantitative maps of the corresponding underlying magnetic susceptibility distribution. QSM is useful for depicting the anatomy and for detecting brain abnormalities. But its utility in the context of ischemic stroke has not been extensively characterized. We tested the ability of QSM to characterize tissue changes in the transient middle cerebral artery occlusion (tMCAO) model of cerebral ischemia. We acquired high resolution GRE of mice brains at different time points after tMCAO for computation of QSM and MR frequency maps, and compared these maps with DWI and multi-slice multi-echo imaging acquired with the same animals. Prominent vessels with increased magnetic susceptibility were visible on frequency and magnetic susceptibility maps surrounding the lesion at all times (mostly visible at >12h after reperfusion). Immunohistological examination revealed compressed capillaries and prominent vessels after reestablishing reperfusion may indicate a compensatory effect. In addition, on both contrast maps regions of decreased magnetic susceptibility delineated at 24h and 48h after reperfusion that were distinctly different from the lesions seen on maps of the apparent diffusion coefficient (ADC) and T2 relaxation time constant. Since QSM can be performed without additional acquisition time in the course of acute stroke MRI examination, it may provide complementary information for the diagnostic follow-up of cerebral ischemia.