Abstract Neuronal cell death and microglial changes are both hallmarks of neurodegenerative disorders. Therefore, analysis of degenerating neurons related to microglial changes are addressed in many studies of neurosciences. Here we compared different lesion models and two markers for neurodegeneration (Fluoro-Jade and propidium iodide) in an in vivo as well as an in vitro approach. Fluoro-Jade is a specific and selective marker to identify neurons undergoing degeneration. We also tested this marker to analyze neurodegeneration in organotypic hippocampal slice cultures. We could show that activation of microglia is followed by neuronal cell death. Most degeneration markers, such as propidium iodide, only stain the neuronal cell body excluding the axonal and dendritic processes. Fluoro-Jade is able to stain the distal portion as well as the proximal portion of the dissected axon including the axotomized neuron, as so called anterograde and retrograde degeneration after axotomy. To analyze the specificity of Fluoro-Jade, we used primary microglial and BV-2 cells, a well-described murine microglial cell line. Treatment of microglial and BV-2 cells with an excess of l-glutamate induces cell death which could be detected by propidium iodide staining, but not by Fluoro-Jade, demonstrating its specificity to monitor neuronal cell death.