The vascular structure of cavernous malformations (CMs) and arteriovenous malformations (AVMs) is different and they have differing clinical responses to radiosurgery. The structural differences of irradiated and non-irradiated CMs and AVMs were examined to clarify their differential responses to radiosurgery. CMs showed a greater ratio of intraluminal diameter to vessel wall thickness and a lack of subendothelial fibroblasts, myofibroblasts and smooth muscle cells compared with AVMs. Partial proteinaceous clots (19–22% of lumen) formed in CM sinusoids after radiosurgery but complete vaso-occlusion did not occur for up to 6 years after radiosurgery. In contrast, complete vaso-occlusion (91–98% of lumen) by fibrin thrombi that are permanent clots was observed in AVM vessels. Radiation-induced neuronal loss, neurofibrillary degeneration of neurons and myelin fragmentation were typical in the surrounding brain tissue of the irradiated lesions. The different structure and cellular composition of CMs and AVMs is likely to influence their responses to radiosurgery.