Spot blotch caused by Cochliobolus sativus has been the major yield-reducing factor for barley production during the last decade. In this study, a systematic sequencing of expressed sequence tags (EST) was chosen to obtain a global picture of the assembly of genes involved in pathogenesis. To identify a large number of plant EST, which are induced at different time points, an amplified fragment length polymorphism display of complementary DNA was utilised. Transcriptional changes of 456 EST were observed, of which 22 have no previously described function. On one hand, EST-annotations showed homologies to a number of classical pathogenesis-related or PR genes that play a role in the signal transduction pathway. However, a notable number of EST were derived from hypothetical protein-coding genes with no clear domain sequence identity. Hence, the transcriptomic approach presented here constitutes no prior assumption about the genes activated during the C. sativus-barley interaction.