Background: Chronic kidney disease (CKD) is common in patients with heart failure, and often results in left ventricular diastolic dysfunction (LVDD). However, the mechanisms responsible for cardiac damage in CKD-LVDD remain to be elucidated. Epigenetic alterations may impose long-lasting effects on cellular transcription and function, but their exact role in CKD-LVDD is unknown. We investigate whether changes in cardiac site-specific DNA methylation profiles might be implicated in cardiac abnormalities in CKD-LVDD. Methods: CKD-LVDD and normal control pigs (n=6 each) were studied for 14 weeks. Renal and cardiac hemodynamics were quantified by multidetector CT and echocardiography. In randomly selected pigs (n=3/group), cardiac site-specific 5-methylcytosine (5mC) immunoprecipitation (MeDIP)- and mRNA-sequencing (seq) was performed, followed by integrated (MeDiP-seq/mRNA-seq analysis), and confirmatory ex vivo studies. Results: MeDIP-seq analysis revealed 261 genes with higher (fold-change>1.4; p<0.05) and 162 genes with lower (fold-change<0.7; p<0.05) 5mC levels in CKD-LVDD versus normal pigs, which were primarily implicated in vascular endothelial growth factor (VEGF)-related signaling and angiogenesis. Integrated MeDiP-seq/mRNA-seq analysis identified a select group of VEGF-related genes in which 5mC levels were higher, but mRNA expression lower in CKD-LVDD versus normal pigs. Cardiac VEGF signaling gene and VEGF protein expression was blunted in CKD-LVDD compared to controls and associated with decreased subendocardial microvascular density. Conclusions: Cardiac epigenetic changes in VEGF-related genes are associated with impaired angiogenesis and cardiac microvascular rarefaction in swine CKD-LVDD. These observations may assist in developing novel therapies to ameliorate cardiac damage in CKD-LVDD.