Retinal ganglion cells (RGCs) regenerating through peripheral nerve grafts show enhanced survival after further axonal injury for at least 4 weeks [Restor. Neurol. Neurosci. 21 (2003) 11]. Here, we examined the survival of the neurons and their microglial phagocytosis in dependence of the site of reaxotomy. Therefore, the optic nerve in adult rats was transected at different distances from the eye cup and replaced with an autologous piece of sciatic nerve. After 14 days of axonal growth, the regenerated neurites were reaxotomized either within the remaining optic stump or within the graft and their cell bodies were retrogradely labeled. Reaxotomy of regenerated ganglion cells within the remaining optic nerve resulted in reduced (but not significant) ganglion cell survival and significant microglial phagocytosis in contrast to reaxotomy within the peripheral nerve graft. Furthermore, phagocytosis-dependent labeling using two different fluorescent tracers revealed that the same microglial cell can phagocytose further dying ganglion cells within 14 days after the first activation. The results suggest that the intrasciatic segments of axons receive some trophic support that is retrogradely transported and required to limit the microglial activation. The microglial capability to phagocytose dying neurons several fold emphasizes their function in permanent scavenging within the retina.