To provide a global analysis of the influence of Tau neuropathology at molecular level, we used cDNA arrays representing 8832 genes to determine the mRNA expression profile in transgenic mice expressing the most common frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17) Tau mutation (P301L) (Nat. Genet. (2000) 402). Genes whose expression is associated with development of neurofibrillary tangles and neuron loss in P301L mice with motor and behavioral deficits were identified. The data suggest that a major mechanism underlying P301LTau neurodegeneration primarily involved altered expression of genes contributing to inhibition of apoptosis and intracellular transport. We propose that the expression of mutated P301L may lead to select altered expression of genes which may cause neurodegeneration in FTDP-17.