Cardiac hypertrophy is a complex and nonhomogenous response to various stimuli. In this study, we used high-density oligonucleotide microarray to examine gene expression profiles during physiological hypertrophy, pathological hypertrophy, and heart failure in Dahl salt-sensitive rats. There were changes in 404/3,160 and 874/3,160 genes between physiological and pathological hypertrophy and the transition from hypertrophy to heart failure, respectively. There were increases in stress response genes (e.g., heat shock proteins) and inflammation-related genes (e.g., pancreatitis-associated protein and arachidonate 12-lipoxygenase) in pathological processes but not in physiological hypertrophy. Furthermore, atrial natriuretic factor and brain natriuretic protein showed distinctive changes that are very specific to different conditions. In addition, we used a resampling-based gene score-calculating method to define significantly altered gene clusters, based on Gene Ontology classification. It revealed significant alterations in genes involved in the apoptosis pathway during pathological hypertrophy, suggesting that the apoptosis pathway may play a role during the transition to heart failure. In addition, there were significant changes in glucose/insulin signaling, protein biosynthesis, and epidermal growth factor signaling during physiological hypertrophy but not during pathological hypertrophy. atrial natriuretic factor; brain natriuretic protein; insulin; apoptosis; microarray CARDIAC HYPERTROPHY is a complex response to various hypertrophic signals that promote the growth of cardiac myocytes. Multiple neurohumoral, hormonal, and mechanistic stimuli have been implicated in, and numerous interdependent pathways and molecules shown to be associated with, cardiac hypertrophy (10, 37). Accordingly, the responses of cardiac myocytes to different hypertrophic stimuli are not homogenous. Examples of stimulus-dependent hypertrophic responses can be found in both physiological and pathological hypertrophy. Exercise-induced cardiac hypertrophy is a good example of physiological hypertrophy, which is a favorable adaptive response of the heart to increases in bodily demand (8). In comparison, pathological hypertrophy is a maladaptive response to pathological stimuli, such as pressure or volume overload. These differences are particularly evident clinically, for pathological hypertrophy often progresses to heart failure, especially when pathological stimuli are persistent, whereas physiological hypertrophy usually does not. These examples support the notion that cardiac hypertrophies are not all the same, and suggest that stimulus-specific hypertrophic responses may be associated with distinct molecular changes (20,27).Previous studies of models of cardiac hypertrophy, using microarray technology, have yielded interesting but varied results (1,4,13,16,19,23,31,32,34,50,54). Studies of putative physiological stimuli showed increased expression of genes involved in the cell cycle, cell structure, intracellular signaling, protein s...