Interleukin 6 (IL-6) is a major mediator of the cytokine storm during shock. Its actions on the endothelium lead to pathological vascular leakage, leukocyte adhesion, and coagulopathy, which may result in multiorgan dysfunction and potentially death. Many shock survivors suffer long-term sequelae. We hypothesize that shock-induced endothelial epigenetic changes are involved in orchestrating these chronic pathological changes. Here, we interrogated the DNA methylation changes in the kidney endothelium after a challenge with lipopolysaccharides (LPS) in wilt type (WT) mice and in mice lacking endothelial SOCS3 (SOCS3iEKO). We identified 2596 differentially methylated positions (DMP) after an LPS challenge in WT mice. Notably, lack of endothelial SOCS3 leads to a highly divergent response, with 3564 DMP in response to LPS in SOCS3iEKO vs WT mice. Consistent with the hyper-inflammatory response in SOCS3iEKO mice, gene ontology analysis shows an enrichment in genes associated with an inflammatory response. To assess whether endothelial cells respond to IL-6 signaling directly by inducing DNA methylation changes, we challenged human umbilical vein endothelial cells in culture with IL-6 for 72 hours prior to methylomics assays. DNA methylation modifications were observed in sites associated with pathways regulating the regulation of cell adhesion, proliferation, and cytokine signaling. To determine the stability of these changes, we treated cells with IL-6 for 72h, followed by 96h in the absence of IL-6. We found that 40% of the DMP remained modified after the cytokine wash with a mean difference of less than 2% when comparing washed (72+96h) vs. non-washed cells (72h alone), suggesting that many changes in the endothelial methylome may remain in place for prolonged periods. In summary, persistent activation of endothelial IL-6 signaling leads to endothelial DNA methylation changes. Together, our data demonstrate that in response to pro-inflammatory stimuli, the endothelium elicits epigenetic changes that are at least in part due to IL-6/STAT3/SOCS3 signaling. These changes may regulate pathways associated with reduced long-term survival and chronic organ damage after shock.