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Acute heat stress is common in aquaculture and can affect diverse physiological processes in fish; however, different species of fish have various mechanisms for heat stress adaptation. In this study, we profiled the transcriptome responses of the Atlantic salmon (Salmo solar) to heat stress at 23 degrees C for 6 or 24 h, compared with that of fish at a normal temperature of 13 degrees C. The liver was selected as the target tissue for this analysis. A total of 243 and 88 genes were differentially expressed after 6 and 24 h of heat stress, respectively. Of these, only 22 were common to both time points, and most of these common genes were molecular chaperones such as heat shock cognate 71 kDa protein and heat shock protein 90-alpha. Genes such as activating transcription factor 6, calreticulin, protein disulfide isomerase A3, and protein kinase R-like endoplasmic reticulum kinase-eukaryotic initiation factor 2-alpha were only up-regulated after 6 h of heat stress; most of these genes are involved in the endoplasmic reticulum stress pathway. Indeed, endoplasmic reticulum stress was identified at 6 h but not at 24 h, suggesting that stress response plays an important role in the adaptation of Atlantic salmon to acute heat stress. Other up-regulated genes at 6 h were related to the insulin and nucleotide oligomerization domain-like receptor signaling pathways, which directly eliminate misfolded proteins and sustain sugar and lipid homeostasis. At 24 h, heat stress influenced the expression of steroid and terpenoid backbone biosynthesis, which may influence the sexual development and differentiation of Atlantic salmon. Overall, our results elucidate the transcriptome mechanisms that contribute to short-term heat tolerance in the liver of Atlantic salmon.