Abstract Hemodynamics creates a constantly changing physical and chemical environment to which the arterial endothelium is exquisitely sensitive. Biomechanical stresses are intrinsic to blood flow characteristics and blood pressure and therefore are important considerations in hypertension. Near branching anatomical sites in arteries, blood flow separates from the main flow to undergo complex multi-directional characteristics for a part of each cardiac cycle (collectively referred to as disturbed flow). Atherosclerosis and aneurysmal pathology develop preferentially at disturbed flow locations, particularly when an additional cardiovascular risk factor such as hypercholesterolemia or high blood pressure are present. In the pre-disease state, a pre-inflammatory endothelial phenotype is characteristically present in such regions in contrast to nearby endothelium outside of the complex disturbed flow fields. A regulatory hierarchy of mechanisms controls endothelial gene and protein expression (and function) in response to the flow environment. Gene expression regulation, the transcription of the DNA (genomic) code to mRNA, is well described by transcription factors, enhancers and repressors, many of which are flow responsive. However, emerging studies describe the additional role of localized disturbed blood flow upon epigenetic mechanisms of endothelial responses to biomechanical stress. Epigenetics and epigenomics (global analyses of epigenetic changes across the entire genome) encompass heritable and non-heritable changes in nuclear chromatin leading to gene expression changes that cannot be attributed to changes in the primary DNA sequence. Hemodynamic stimuli have recently been shown to induce epigenetic responses including transcriptional regulation by proximal promoter DNA methylation, and regulation of gene and protein expression by histone/chromatin remodeling and by noncoding RNA-based mechanisms.Dynamic epigenomic responses to flow that result in regulation of endothelial gene expression in vivo and in vitro include: (i) regions of stable differentially methylated DNA in swine and mouse endothelial genomes that are arterial site-specific and map to atherosusceptibility, (ii) disturbed flow (but not undisturbed flow) applied to endothelial cells in vitro that induces DNA methylation through DNA methyltransferase enrichment of gene promoter regions; the resulting hypermethylation suppresses gene expression, (iii) histone acetylation / deacetylation and methylation that create histone marks that enable or suppress gene expression by controlling access of transcription factors to chromatin DNA, and (iv) short microRNAs and long noncoding RNAs that interact with highly specific binding sites of newly synthesized mRNA to promote its degradation and thus suppress transcription. Flow-mediated epigenomic responses intersect with cis and trans factor regulation to maintain endothelial function in a shear-stressed or pressure-stressed environment and may contribute to localized endothelial dysfunctions that promote localized vascular pathology.The Encyclopedia of DNA Elements (ENCODE) and the International Human Epigenome Consortia (IHEC) have uncovered thousands of putative epigenetic regulatory sites in non-coding regions of the genome. Methylation of cytosine nucleosides in DNA both at/near gene promoter regions as well as at some distance upstream is a potent epigenetic suppressor of transcription. Recently, complete methylated DNA immunoprecipitation sequencing (MeDIP-seq) of regions of arterial endothelium associated with disturbed vs undisturbed flow in vivo in pigs has identified many differentially methylated DNA profiles enriched in exons and 5'UTR sequences of annotated genes, 60 of which are linked to cardiovascular disease. Furthermore, in human arterial endothelial cells in culture we have demonstrated DNA methylation plasticity to be regulated by disturbed flow resulting in suppression (hypermethylation) or stimulation (hypomethylation) of transcription. We propose dynamic DNA methylation to be a genome-wide epigenetic mechanism of transcriptional control that regulates adaptive endothelial phenotype plasticity in response to the local environment, including biomechanical stresses associated with disturbed flow characteristics and hypertension.The epigenomic code therefore has the potential to figure prominently in disease susceptibility and pathogenesis arising from environmental influences independent of, or in concert with, mutations and single nucleotide polymorphisms (SNP) linked to many complex diseases, including hypertension and cardiovascular disease. The role of disturbed flow as a hemodynamic regulator of epigenomic DNA methylation-mediated and histone-mediated gene expression may play a prominent role in endothelial vascular function and dysfunction in hypertension, atherogenesis and aneurysm development. The cellular mechanisms that link hemodynamics and biomechanical stress to the epigenomic code remain unexplored.