Heart disease is the major cause of death in diabetes, a disorder characterised by chronic hyperglycemia and cardiovascular complications. Diabetic cardiomyopathy (DCM) is increasingly recognised as a major contributor to diastolic dysfunction and heart failure in diabetes but its molecular basis has remained obscure, in part because of its multi-factorial origins. Here we employed comparative transcriptomic methods with quantitative verification of selected transcripts by RTqPCR to characterise the molecular basis of DCM in rats with STZ-induced diabetes of 16-weeks' duration. Diabetes caused left ventricular disease that was accompanied by significant changes in the expression of 1614 genes, 749 of which had functions assignable by Gene Ontology classification. Genes corresponding to proteins expressed in mitochondria accounted for a disproportionate number of those whose expression was significantly modified in DCM, consistent with the idea that the mitochondrion is a key target of the pathogenic processes that cause myocardial disease in diabetes. Diabetes also induced global perturbations in the expression of genes regulating cardiac fatty acid metabolism, whose dysfunction is likely to play a key role in the promotion of oxidative stress, thereby contributing to the pathogenesis of diabetic myocardial disease. In particular, these data point to impaired regulation of mitochondrial -oxidation as central in the mechanisms that generate DCM pathogenesis. This study provides a comprehensive molecular snapshot of the processes leading to myocardial disease in diabetes.