In G93A mice, the most popular model of amyotrophic lateral sclerosis (ALS), neuronal Lewy-body-like hyaline inclusions (LBHIs) and mitochondria-derived vacuoles are observed in addition to motor neuron loss. Although LBHIs are thought to be toxic, the significance of the mitochondria-derived vacuoles has not been fully investigated. In this study, the relationship between the formation of these vacuoles and LBHIs was clarified statistically in the lumbar segment from two phyletic lines of G93A mice (G1L, G1H), using immunohistochemical methods. Furthermore, the distributions of vacuoles and LBHIs were examined in the pons including the facial nucleus, where pathological changes occur in ALS patients and G93A mice. Numerous vacuoles 2-3 microm in diameter were detected in the neuropil of the lumbar segment from G1L mice euthanatized approximately 3.5 months prior to the onset of the disease. Most of the vacuoles disappeared, but some became larger as the disease progressed. The number of vacuoles with a diameter exceeding 5 microm began to decrease after disease onset, while that of intra-neuritic LBHIs increased rapidly. There was a strong inverse correlation between the numbers of vacuoles and LBHIs in symptomatic mice (P<0.01; G1L, r=-0.91; G1H, r=-0.93). In the facial nucleus of G1L mice, where the number of motor neurons was significantly reduced, only a few LBHIs were detected along with prominent vacuole formation. In contrast, significantly more LBHIs with little vacuole formation were evident around the facial nucleus in G1L mice. Furthermore, the SOD1 immunoreactivity in vacuoles initially increased and then decreased after disease onset. Taken together, the present findings suggest that the mitochondria-derived vacuoles might prevent the formation of LBHIs by sequestering mutated SOD1 from the cytoplasm.