The peritrophic matrix (PM) performs several functions including the compartmentalization of digestion, the regulation of nutrient uptake and as a barrier to pathogen infection; however, the specific components responsible for these functions are poorly defined. Only 3 types of PM proteins have been identified from Lepidoptera; insect intestinal mucin and peritrophins with either multiple chitin binding domains or a chitin deacetylase-like domain. A model based on this limited information illustrates the proposed contribution of two proteins to PM structure has been developed but it does not address the mechanisms by which the PM performs its disparate functions. We employed genomics and proteomic approaches to survey the proteins expressed by the midgut epithelium that associate with the Mamestra configurata (bertha armyworm) PM. Our approach has been to couple 1 and 2-dimensional gel separation of PM proteins with MALDI-mass spectrometry to generate de novo sequence information for specific PM proteins. In parallel, ca. 3900 ESTs were generated from a midgut cDNA library yielding a database of genes expressed in the midgut. Bioinformatics tools were used to link the data sets (peptide and cDNA sequences) leading to the identification of genes corresponding to several new PM proteins. This information was used to create a revised model of PM structure. This research will ultimately lead to the identification of proteins that can serve as targets for “designer” insect control molecules, as well as to further our understanding of insect midgut physiology and digestive biochemistry.