Cold-acclimated (CA) phenotype of trout heart was induced by 4 weeks acclimation at 4°C and was characterized by 32.7% increase in relative heart mass and 49.8% increase in ventricular myocyte size in comparison to warm-acclimated (18°C) fish (p<0.001). Effect of temperature acclimation on transcriptome of the rainbow trout heart was examined using species-specific microarray chips containing 1380 genes. After 4 weeks of temperature acclimation, 8.8% (122) of the genes were differently expressed in CA and WA hearts, and most of them (82%) were up-regulated in the cold (p<0.01). Transcripts of genes engaged in protein synthesis and intermediary metabolism were most strongly up-regulated, whereas genes contributing to the connective tissue matrix were clearly repressed. Extensive up-regulation of the genes coding for ribosomal proteins and translation elongation and initiation factors suggests that the protein synthesis machinery of the trout heart is enhanced in the cold and is an essential part of the compensatory mechanism causing and maintaining the hypertrophy of cardiac myocytes. The prominent depression of collagen genes may be indicative for a reduced contribution of extracellular matrix to the remodeling of the CA fish heart. Temperature-related changes in transcripts of metabolic enzymes suggest that at mRNA level glycolytic energy production from carbohydrates is compensated in the heart of CA rainbow trout while metabolic compensation is absent in mitochondria. In addition, the analysis revealed three candidate genes - muscle LIM protein, atrial natriuretic peptide B and myosin light chain 2 - which might be central for induction and maintenance of the hypertrophic phenotype of the CA trout heart. These findings indicate that extensive modification of gene expression is needed to maintain the temperature-specific phenotype of the fish heart.