When the neural tracer Fluoro-Gold is used to retrogradely label a population of axotomized neurons, cellular labeling can persist in the axotomized nucleus even when Nissl staining indicates that the injured neurons have degenerated. In order to determine the identity of the labeled cells that remain, this study combines retrograde transport of Fluoro-Gold with immunocytochemical methods for identification of specific non-neuronal cell types following peripheral axotomy and Fluoro-Gold labeling of motoneurons in the dorsal motor nucleus of the vagus in neonatal and adult rats. Fourteen days following cervical vagotomy in neonatal rats, Nissl staining revealed a virtually complete loss of vagal motoneurons. Fourteen days after cervical vagotomy in adult rats, vagal motoneuronal loss was not yet extensive but chromatolysis had clearly begun. Injection of Fluoro-Gold into the vagus nerve just prior to the vagotomy led to Fluoro-Gold labeling of remaining vagal motoneurons. In addition, many other small, brightly labeled cells were present in the lesioned vagal nuclei of all rats. Immunofluorescent identification of astrocytes with anti-glial fibrillary acidic protein and microglia and macrophages with OX42 (anti-C3bi complement receptor) and ED1 (anti-monocyte/macrophage cytoplasmic antigen) demonstrated that the small, bright Fluoro-Gold-labeled cells were non-neuronal, non-astrocytic phagocytes, including microglia. These results indicate that phagocytic microglia and other macrophages sequester Fluoro-Gold in the axotomized dorsal motor nucleus of the vagus of neonatal and adult rats, leading to persistence of fluorescent cellular labeling following the loss of retrogradely labeled axotomized neurons.