We used magnetic resonance (MR) imaging to evaluate the secondary degeneration in remote areas, such as the ipsilateral thalamus and the substantia nigra, after cerebral infarction in the territory of the middle cerebral artery (MCA). The ventral nuclei of the ipsilateral thalamus were visualized as low-signal-intensity regions on proton-density-weighted images (PDWIs) and/or T2-weighted images (T2WIs) as early as 8 days, but mostly a few weeks after cortical infarction. On the other hand, an area of high signal intensity on T2WIs of the dorsomedial nucleus of the ipsilateral thalamus appeared approximately 6 weeks after onset. The lesion in the ipsilateral substantia nigra was manifested as a high intensity signal on PDWIs and T2WIs, an average of 14 days after the striatal infarction. These results coincide quite well with our observations in experimental studies.