The purpose of this study was to examine mitochondrial changes in the spinal cord of transgenic mice of a relatively low transgenic copy number (gene copy 10) expressing a G93A mutant human Cu/Zn superoxide dismutase (SOD1) that were generated in our own laboratories by electron and immunoelectron microscopy from presymptomatic to symptomatic stages. Age-matched non-transgenic mice served as controls at each stage. Ultrastructurally, at the early presymptomatic stage, many mitochondria in large myelinated axons exhibited swelling with an increased number of cristae, and bore small vacuoles in the matrix, cristae or both, in the anterior root exit zone, anterior root, and in the neuropils of the ventral portion of the anterior horn. At the late presymptomatic stage, vacuoles of various sizes (including large ones) were observed in the same regions as in the previous stage. The intermembrane space of mitochondria was also vacuolated. In mitochondria with advanced vacuolation, the vacuolar space was filled with a granular or amorphous substance. At the symptomatic stage, mitochondrial vacuolation seen in the late presymptomatic stage persisted, although to a lesser extent. These vacuolated mitochondria were predominantly seen in the axons, but not in the somata of normal-looking neurons or dendrites at any stage, which differs from that described in other reports. Non-transgenic littermates occasionally exhibited vacuolar changes in the axons of anterior horns. However, they were smaller both in size and number than those in transgenic mice. By immunoelectron microscopy using an immunogold labeling method, at the presymptomatic and symptomatic stages both SOD1 and ubiquitin determinants were localized in vacuolated mitochondria, particularly in the granular or amorphous substance of large vacuoles, but were not detected in most normal-appearing mitochondria. The SOD1-immunoreactive mitochondria were exclusively observed in the axons, and not in proximal dendrites or somata. These findings suggest that the toxicity of mutant SOD1 directly affects mitochondria in the axons and increases with the disease progression. Thus, the mutant SOD1 toxicity might disrupt axonal transport of substrates needed for neuronal viability, leading to motor neuron degeneration. The localization of both ubiquitin and SOD1 in vacuolated mitochondria indicates that protein degradation by ubiquitin-proteasomal system may be also disrupted by several pathomechanisms, such as decreased processing of ubiquitinated proteins due to impairment of mitochondrial function or of proteasomal function, both of which are caused by mutant SOD1. Moreover, giant mitochondrial vacuoles occupying almost the entire axonal caliber could be another contributing factor in motor neuron degeneration, in that they could physically block axonal transport.