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We studied Bacillus thuringiensis Cry3Aa intoxication and the expression of insect gut peptidases in Tenebrio molitor larvae. Larvae digest protein by cysteine (papain family) peptidases in the anterior midgut and serine peptidases (chymotrypsin family) in the posterior midgut. The data demonstrate that after 12 h of intoxication, 11/26 cysteine peptidase transcripts were significantly increased in expression (2-4-fold), including the main digestive cathepsin B, but after 24 h these transcripts mostly were decreased. Serine peptidase transcripts included 88 presumably active peptidases and 104 inactive homologs. Thirty two transcripts of 88 significantly changed expression after 12 h intoxication, and changes ranged from approximately 6-fold increase to 20-fold decrease. Expression of the main digestive trypsin and chymotrypsin mRNAs decreased. Among different groups of serine peptidases with altered expression levels, only chymotrypsin-like peptidases were significantly increased after 12 h intoxication. By 24 h, the changes in expression were similar to the 12 h profile. The majority of serine peptidase homolog mRNAs were decreased in expression. The severe change in expression of serine peptidases induced by intoxication may be associated with the close proximity of secreting cells to the lesion focus in the posterior midgut. At the same time, the insect maintained the production of critical digestive cysteine peptidases synthesized and located in the anterior midgut. The data on suppression of insect digestive system after 24 h intoxication correlate to observations of intoxicated larvae and cessation of feeding. The research was performed with the support of the Russian Foundation for Basic Research (grants #14-04-91167-NSFC_а and #12-04-01562-а).