Lignocellulose digestion in the lower termite Reticulitermes flavipes is mediated by enzymes of both endosymbiont and termite origin. In order to detail the molecular basis of the endogenous digestion process associated with the termite genome, we have initiated an expressed sequence tag (ESTs) survey of the R. flavipes gut transcriptome. A normalized cDNA library was generated from symbiont-free dissected worker termite guts (approximately 2000 guts=1g of tissue). High-quality ESTs have been obtained from this library, representing numerous putative gene transcripts. The transcripts were functionally annotated based on similarity to gene sequences from Drosophila melanogaster and from other insects. Similarity searches identified several genes homologous to lignases, cellulases, glucanases, glucosidases, xylanases and associated proteins, confirming our hypothesis that the gut-specific library may contain a full complement of termite-genome-derived genes that collaborate to accomplish lignocellulose digestion and assimilation within the termite gut.