The synaptic terminals' withdrawal from the somata and proximal dendrites of injured motoneuron by the processes of glial cells following facial nerve axotomy has been the subject of research for many years. This phenomenon is referred to as synaptic stripping, which is assumed to help survival and regeneration of neurons via reduction of synaptic inputs. Because there is no disruption of the blood–brain barrier or infiltration of macrophages, the axotomy paradigm has the advantage of being able to selectively investigate the roles of resident glial cells in the brain. Although there have been numerous studies of synaptic stripping, the detailed mechanisms are still under debate. Here we suggest that the species and strain differences that are often present in previous work might be related to the current controversies of axotomy studies. For instance, the survival ratios of axotomized neurons were generally found to be higher in rats than in mice. However, some studies have used the axotomy paradigm to follow the glial reactions and did not assess variations in neuronal viability. In the first part of this article, we summarize and discuss the current knowledge on species and strain differences in neuronal survival, glial augmentation and synaptic stripping. In the second part, we focus on our recent findings, which show the differential involvement of microglia and astrocytes in synaptic stripping and neuronal survival. This article suggests that the comparative study of the axotomy paradigm across various species and strains may provide many important and unexpected discoveries on the multifaceted roles of microglia and astrocytes in injury and repair.