The UK Atlantic salmon aquaculture industry must meet a number of challenges if it is to remain sustainable and profitable. Important constraints on commercial production include a.) the supply of dioxin-free highly unsaturated oils for the salmon diet, b.) protein growth efficiency, c.) infectious disease, and d.) a long and complex lifecycle. TRAITS (TRanscriptome Analysis of Important Traits in Salmon), a BBSRC funded project initiated in 2003, was founded on the premise that gene expression monitoring can be developed as a user-friendly means of assessing health and performance. The project is a partnership involving three UK universities (Aberdeen, Cardiff and Stirling) and the Norwegian Salmon Genome Project (NSGP), supported by ARK-Genomics and working in collaboration with Operon and Marine Harvest (a division of Nutreco). It is linked to the salmon farming industry through Scottish Quality Salmon, an organisation representing a majority of producers in the UK. The goal of TRAITS is to develop an oligonucleotide array for probing key elements of the transcriptome involved in polyunsaturated fatty acid metabolism, protein catabolism, responses to bacterial and viral challenge, and the process of freshwater to seawater adaptation (smoltification). We report here on a preliminary deliverable of this project, a 17K gene Atlantic salmon cDNA microarray. Details of its construction and preliminary verification are presented. The microarray, and associated resources, are available through ARK-Genomics (http://www.ark-genomics.org).