The mouse mutant SOD1G93A is a model of ALS, a neurological disorder characterized by progressive loss of upper and lower motor neurons. In the preclinical stage and during the progression of the clinical symptoms of this mouse mutant we investigated the fatigability of monosynaptic reflex transmission, the activity/reactivity of microglia (MG) and astrocytes (AG) and the influence of methylene blue (MB) on MG–induced inflammation and motoneurone degeneration. The later investigations were performed by 2-photon laser scanning microscopy in ALS mice with additional expression of cell type specific fluorescent proteins (MG: EGFP; neurons: EYFP; AG:ECFP). (1) The fatigability of monosynaptic reflex transmission increased not before the development of clinical symptoms.(2) In contrast to the delayed reaction in wild type (WT) mice AG contribute to the rapid response of non-neuronal cells to axonal lesions in ALS mice. (3) In the affected lateral spinal tract of ALS mice, different phases of microglia-mediated inflammation were observed: highly reactive microglial cells in preclinical stages and morphologically transformed microglia that have lost their function of tissue surveillance and injury-directed response in clinical stages. Macrophages of the peripheral nervous system of ALS mice lack any substantial morphological reaction despite distinct preclinical degeneration of peripheral motor axons and neuromuscular junctions. (4) Locally at the spinal cord applied MB can suppress inflammatory events in ALS mice. There was evidence that systemic MB application in these mice may delay disease onset via neuroprotection, whereas it was not able to reduce the progression. The findings confirm that glia may play an important role for the progression of ALS during certain stages.