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During atrial fibrillation (AF), rapid stimulation causes atrial remodeling that increases arrhythmia susceptibility. Using an established atrial (HL-1) myocyte model, we investigated the transcriptional profile associated with early atrial myocyte remodeling. Spontaneously contracting HL-1 cells were cultured in the absence and presence of rapid stimulation for 24 h and RNA harvested for microarray analysis. We identified 758 genes that were significantly altered with rapid stimulation (626 up- and 132 down-regulated). Results were confirmed using real-time quantitative RT-PCR for selected genes based on physiological relevance in human AF and/or experimental atrial tachycardia (AT), and regulation in the microarray results. In some cases, transcriptional changes were rapid, occurring within 3 h. For a selected group of genes, results were validated for the expressed protein, with findings that correlated with observed transcriptional changes. Significantly regulated genes were classified using the Gene Ontology Database to permit direct comparison of our findings with previously published myocardial transcriptional profiles. For broad functional categories, there was strong concordance between rapidly stimulated HL-1 myocytes and human AF, but not for other remodeling paradigms (cardiomyopathy and exercise). Many individual gene changes were conserved with AF/AT, with marked up-regulation of genes encoding brain and atrial natriuretic peptide precursors, and heat shock proteins. For the conserved genes, both a cellular stress and survival response was evident. Our results demonstrate similarities with human AF/experimental AT with respect to large-scale patterns of transcriptional remodeling, as well as regulation of specific individual genes. Importantly, we identified novel pathways and molecules that were concordantly regulated in vivo.