Neurospora crassa is a filamentous ascomycete fungus that has been a model organism for understanding gene regulation and gene function for over 80 years. Biochemical and molecular tools are well developed with this organism and include a complete genome sequence (Galagan et al., Nature 2003), full genome microarrays and ~5000 single gene deletion strains; ~8000 mutants will be available by 2009 (http://www.dartmouth.edu/~neurosporagenome/). In nature, N. crassa grows on burnt and composted plant material, including sugarcane. It has been known for over 30 years that N. crassa has the capability of producing lignocellulolytic enzymes, which can degrade both lignin and cellulose. Miscanthus giganteus has been designated as a promising crop for the development of plant-derived biofuels by the Department of Energy. Computational predictions and transcriptional profiling data show that at least 509 genes in the Neurospora genome encode proteins that are predicted to be secreted; this dataset in enriched for lignin degradation enzymes and cell wall deconstruction enzymes such as cellulases. N. crassa can grow on Miscanthus as a sole carbon source. To define the global regulatory mechanisms associated with Miscanthus cell wall deconstruction by N. crassa, we have performed comprehensive time-course analysi of gene expression patterns using transcriptional profiling and full genome microarrays for N. crassa. Mutational and proteomics approaches are currently being used to characterize the regulatory network associated with plant cell wall deconstruction in N. crassa.