The survival of the bovine lungworm Dictyocaulus viviparus, one of the most important parasites in cattle, inside the host is ensured by arrested development during adverse environmental conditions, commonly referred to as hypobiosis. In the present study, a subtractive hybridization approach was used to compare the transcription profiles of hypobiotic and non-hypobiotic larvae (L5hyp and L5, respectively). Thereby, 75 L5hyp-enriched and 58 L5-enriched representative ESTs (rESTs) were identified. Subsequent sequence similarity search revealed that 28 L5hyp-rESTs and 11 L5-rESTs were homologous to known transcripts, whereas 47 L5hyp-rESTs and 47 L5-rESTs showed no homologies with published sequences, thus possibly representing parasitic or even Dictyocaulus-specific genes. The differential transcripts were predicted to be involved in nucleic acid synthesis, DNA binding, metabolic pathways and signal transduction. Overall, data presented in this paper provide a first basis for further characterization and analysis of genes driving normal as well as arrested (hypobiotic) parasite development.