To understand the transcriptional response of Ephestia kuehniella caterpillars to parasitization by the endoparasitic wasp Venturia canescens, we examined patterns of gene expression in parasitized and unparasitized host caterpillars using the cDNA-AFLP (cDNA-amplified fragment length polymorphism) technique. Among the approximately 1860 cDNA-fragments detected by using 88 different AFLP primer combinations, we identified 13 transcripts in parasitized caterpillars that showed a suppressed expression pattern with cDNA-AFLP results being confirmed by virtual Northern blot or RT-PCR analysis. Apparently, two different wasp genotypes (RP, RM) seem to differ in their ability to regulate host physiology with regard to suppression of certain genes. Sequence analysis of the cDNA fragments revealed that some of the respective genes are likely to be involved in energy metabolism, protein synthesis, or in signal transduction. In addition, one sequence corresponds to a gene encoding the lepidopteran silk protein fibroin. The putative function of these genes in the interactions between endoparasitoids and their host insects is discussed.