Mitochondria play a central role in cell survival, and apoptotic cell death is associated with morphological changes in mitochondria. Quantification of the morphological and mechanical property changes in brain mitochondria is useful for evaluating the degree of ischemic injury and the neuroprotective effects of various drugs. This study was performed to investigate the changes in brain mitochondria in an 11-vessel occlusion ischemic model treated with magnesium sulfate (MgSO4), utilizing atomic force microscopy (AFM). Rats were randomly divided into three groups consisting of sham (n=6), global ischemia (GI, n=6), and MgSO4-treated global ischemia (MgSO4, n=6). The biophysical properties of brain mitochondria determined from AFM topographic images and adhesion force from force-distance measurements. The mean perimeter of ischemic mitochondria significantly increased to 2,396±541 nm (vs. 1,006±318 nm in control group, P<0.001). The MgSO4 treatment during global ischemia reduced the perimeter of ischemic mitochondria (1,127±399 nm, P<0.001). The other parameters including length, width and area were significantly different than the GI group. Besides, the adhesion force (23.2±3.9 nN) of isolated mitochondria from the MgSO4 group was close to normal levels (28.5±2.5 nN), compared with that of ischemic ones (17.7±3.3 nN, P<0.001). To confirm the neuroprotective effects of MgSO4, we performed Nissl staining. This study suggested that quantitative analysis of mitochondrial changes utilizing AFM could be effective for evaluating neuronal injury and drug effects.