Trimethyltin (TMT) is a neurotoxicant that produces a specific pattern of neuronal degeneration in the hippocampus. In mice, TMT induces a selective neuronal loss of dentate granule cells, astrocyte hypertrophy, and microglia activation. Previous studies in our laboratory demonstrated an early elevation in TNFα mRNA levels suggesting a role in initiation of the injury response. To investigate the role of TNF in this differential susceptibility of distinct neuronal populations, laser capture microdissection (LCM) was used to isolate cells in either the dentate gyrus (DG) or the CA pyramidal layer. RNA levels for TNFα, TNF receptor (TNFR) 1 and TNFR2 were measured in each distinct LCM region by real time RT–PCR. In control tissue, mRNA levels of TNFR2 and, to a lesser extent, TNFR1 were higher in cells of the DG as compared to the pyramidal cell layer. 24 h post‐TMT, the level of TNFα transcript was elevated. Consistent with the pattern of neuronal susceptibility, levels were significantly greater in the dentate region. While this differential pattern was evident at the time of neuronal necrosis, we examined differential effects at an earlier time point of 6 h. RNA from each region, as obtained by LCM, was amplified by a PCR‐based method, and hybridized to 1176 mouse cDNA arrays. Diverse categories of gene were differently express in the two regions including transcription factors (NEX‐1, LKLF), chemokines (MIP1α and β), G proteins (guanine nucleotide binding proteins) and protein kinase (PKCβ, PKCδ, KCIP1). Thus, prior to any evidence of neurodegeneration, significant alterations were detected in distinct cell regions. These results demonstrate the utility of applying these techniques to examine differential vulnerability of neurons in various models of neurodegeneration.