Pathogenic saprolegniaceae species are among the major disease-causing agents in farmed salmonids and in freshwater fish in general. Recent studies have used high-throughput cDNA-based methods to identify new potential actors of fish defence systems against various bacteria and viruses. However, the response of fish to fungal or fungus-like pathogens is still poorly documented. Here, we used a 16,006-gene salmonid cDNA microarray to identify genes which transcription levels are modified in juvenile Atlantic salmon (Salmo salar) affected with saprolegniasis compared to healthy fish from the same families. Our results confirmed the importance of non-specific immunity in the response of fish to saprolegniaceae infections and identified both similarities and differences in their genome-wide transcriptional response to oomycetes compared with their responses to bacterial or viral infections. Moreover, several clones with no known homologues were shown to be over-transcribed in infected fish. These may represent as yet unidentified immune-relevant genes in fish.