Lesion size is an important outcome parameter in experimental stroke research. However, most methods of measuring the infarct volume in rodents either require expensive equipment or render the brain tissue unusable for further analysis. We report on an inexpensive, tissue-saving method for quantifying the infarct volume in small rodents. After 3 h of middle cerebral artery occlusion (MCAO) and 24 h of reperfusion in male Wistar rats, the lesion was first identified using MRI with T2-weighted sequences. The infarct was then visualized in unfixed brain cryosections using microtubule associated protein 2 (MAP2)-immunohistochemistry and silver infarct staining. The lesion areas detected by all three different methods completely overlapped. The infarct volume was calculated for each method from the lesion area size on serial sections and the distance between them. Significant differences in lesion size were found between the individual animals (p = 0.000056), but not between different methods (p > 0.05). MAP2 immunohistochemistry is a convenient and valid method to measure stroke lesion volume; in addition 98% of the brain tissue is saved and available for use in further histological, immunohistochemical, and biochemical analysis.