Prostaglandin H synthetases (cyclooxygenases) catalyze the initial reactions leading to prostanoids in animals. They form interesting links between diet and fish physiology as the type and nature of eicosanoids are affected by dietary lipid sources. Their expression is likely to be affected by tissues and environmental conditions leading to altered amount and ratio of eicosanoids. These mechanisms are, however, poorly understood in fish. In the present study, Atlantic salmon Salmo salar L. (1,000 g, 10°C, seawater) were subjected to acute chasing stress. Liver, kidney, spleen, gill, muscle, midgut and hindgut were extracted before and 1 h post-stress and analyzed for mRNA expression of cox1, cox2a and cox2b. Intestinal samples were further sampled over 24 h for both cox expression and analysis of 15 eicosanoids and isoprostanes of the n-3 and n-6 series. Results show a highly variable but consecutively expression of cox1, cox2a and cox2b in most of the tissues analyzed. Low levels were only found for cox2a in liver and cox2b in liver and kidney. The study reveals the general trend that cox1 is about 10 times the level of cox2b, which again is about 10 times the level of cox2a. Cox2b shows the highest level of expression in the gills indicating a possible higher requirement for this protein in gills. Imposing stress to the fish induces a temporal increase in the expression of cox2a in the midgut, while the gene expression of the other genes is not affected in any of the tissues analyzed. There is, however, a general tendency to increased expression of both cox2 genes that merits further studies. Stress had a profound effect on the intestinal eicosanoid content which showed a general decrease in midgut sections after stress that persisted for at least 24 h.