Excitotoxicity is the overexcitation of neurons due to the excessive activation of excitatory amino acid receptors and is thought to be involved in many neurodegenerative states. The manner in which the neuron breaks down during excitotoxicity is still unclear. The current study used the organotypic hippocampal slice culture model to examine the time-dependent loss of the synaptic vesicular protein synaptophysin and the loss of N-methyl-D-aspartate (NMDA) receptor NR1 subunit availability following an excitotoxic insult (20 μM NMDA) to provide a better understanding of the topographical nature of neuronal death following NMDA receptor activation. Significant NMDA-induced cytotoxicity in the CA1 region of the hippocampus (as measured by propidium iodide uptake) was evident early (15 minutes after exposure) while significant loss of the NR1 subunit and synaptophysin was found at later timepoints (72 and 24 hours, respectively), suggesting delayed downregulation or degradation in axons and dendrites as compared to the soma. The addition of the competitive NMDA receptor antagonist 2-amino-7-phosphonovaleric acid (APV) significantly attenuated all NMDA-induced effects. These results suggest that NR1 and synaptophysin levels as measured by immunoreactivity are not reliable indicators of early cell death.