Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder that causes motor neuron degeneration, progressive skeletal muscle atrophy, paralysis, and death. To understand the mechanism of motor neuron degeneration, we have analyzed the clinical disease progression and the pathological changes in a transgenic mouse model for ALS. We found massive mitochondrial vacuolation at the onset of disease. By detailed morphological observations, we have determined that this mitochondrial vacuolation is developed from expansion of mitochondrial intermembrane space and extension of the outer membrane and involves peroxisomes. Lysosomes do not actively participate at all stages of this vacuolation. We conclude that this mitochondrial vacuolation is neither classical mitochondrial permeability transition nor autophagic vacuolation. Thus, this appears to be a new form of mitochondrial vacuolation and we term this as mitochondrial vacuolation by intermembrane space expansion or MVISE.