Objective: Amyotrophic lateral sclerosis (ALS) is an adult-onset neurological disorder, characterized by progressive loss of motor neurons and degeneration of pyramidal tracts. Mutations in the enzyme superoxide dismutase (SOD1) are the most frequent cause of inherited ALS. Transgenic mice expressing various ALS-linked mutations in SOD1 (mSOD1) recapitulate the fatal paralysis seen in human patients. The mSOD1-mediated toxicity is shown to be non-cell-autonomous deriving not only from motor neurons. In particular, microglia and astrocytes substantially contribute to disease progression. The impact of neuroinflammation is still a matter of debate. Methods: We used transgenic SOD1G93A mice containing fluorescently labeled neurons and microglia. 2P-LSM was applied, under in vivo conditions, to analyze microglia-axon interactions within the spinal lateral column. Results: First, we observed a continuous change of microglial morphology towards an ameboid-like shape from preclinical to advanced clinical stages indicating ongoing inflammatory activity. Application of laser-induced axon transection led to significantly increased glial reactions towards the lesion site in preclinical stages. However, this response became significantly reduced in advanced clinical stages coinciding with morphological transformation of microglia. In contrast to the central inflammation by microglia, no inflammatory processes displayed by macrophages could be observed in the PNS. During disease course degenerative changes were, in addition, observed in neuromuscular junctions. Conclusion: Microglial inflammation can be differentiated in distinct phases: i) microglia that are highly overactive in preclinical stages and ii) morphologically activated microglia that lose their target-directed response in advanced clinical stages. During disease course, aberrant microglial reactions promote motor neuron death and disease progression. Neuroinflammation seems to be neglible within PNS.