Cowpea bruchid, when fed on a diet containing the soybean cysteine protease inhibitor soyacystatin N, activates an array of counter-defense genes to adapt to the negative effects of the inhibitor and regain its normal rate of feeding and development. A collection of 1,920 cDNAs was obtained by differential subtraction with cDNAs prepared from guts of the 4th instar larvae of scN-adapted (reared on scN-containing diet) and scN-unadapted (reared on regular scN-free diet) cowpea bruchids. Subsequent expression profiling using DNA microarray and northern blot analyses identified 94 transcript species from this collection that are responsive to dietary scN. scN-Adapted insects over-expressed genes encoding protein and carbohydrate digestive enzymes, probably to help meet its carbon and nitrogen requirements. Up-regulation of detoxification protein and antimicrobial peptide genes may represent a generalized defense response. scN-Down regulated genes reflected physiological adjustments of the cowpea bruchids to scN challenge. A large portion of the responsive genes, presumably involved in carrying out the counter-defense response, were of unknown function. The full-length cDNA of an scN-inducible cathepsin B-like cysteine protease was obtained. Its transcriptional response to scN during larval development contrasts with the pattern of the cathepsin L family, the major digestive enzymes. These results suggest cathepsin B-like cysteine proteases may play a crucial role in cowpea bruchid adaptation to dietary scN.