Obesity increases the risk for cardiomyopathy in the absence of comorbidities. Myocardial structure is modified by dietary fatty acids. Left ventricular (LV) hypertrophy is associated with Western diet consumption, while intake of n-3 polyunsaturated fatty acids (PUFA) is associated with antihypertrophic effects. We previously observed no attenuation of LV thickening following 3 months of docosahexaenoic acid (DHA) supplementation of a Western diet, compared to Western diet intake alone, in rats that had similar weight, adiposity and insulin sensitivity to control animals. The objective of this study was to define LV gene expression in these animals to determine whether diet alone was associated with a physiologic or pathologic hypertrophic response. We hypothesized that Western diet consumption would favor a pathologic or maladaptive myocardial gene expression pattern, and that DHA supplementation would favor a physiologic or adaptive response. Microarray analysis identified 64 transcripts that were differentially expressed (p≤0.001) within one or more treatment comparisons. Using qRT-PCR, 29 genes with fold change ≥ 1.74 were successfully validated; all but 3 had similar directionality to that observed using microarray, and two genes, Ctgf and Ctsm, were differentially expressed according to diet. Western blot analysis was performed on four proteins relevant to myocardial hypertrophy and metabolism. ACOT1, BTG2 and CA3 showed directional change consistent with gene expression. RETSAT, while not consistent with gene expression, was different according to diet, with increased concentrations in Western fed rats compared to control and DHA supplemented animals. Diet did not distinguish a transcriptome reflecting physiologic or pathologic myocardial hypertrophy; further, the modest changes observed suggest that obesity and associated comorbidities may play a larger role than mere dietary fatty acid composition in development of cardiomyopathy.