Abstract Almost all patients with or at high risk of atherosclerosis are treated with statin therapy. However, there remains a high burden of cardiovascular risk in these patients. Indeed, it is now clear that residual inflammatory risk is a stronger predictor of cardiovascular events, cardiovascular death, and all-cause death than residual cholesterol risk (as measured by low-density lipoprotein cholesterol). Therefore, in this study we sought to better understand the origin of inflammatory residual risk associated with previous exposure to high cholesterol. Tissue resident macrophages and bone marrow derived macrophages (BMDM) from mice which have been exposed to high cholesterol display an augmented polarisation profile. BMDM’s generated ex vivo are grown under standard condition so any effects come from in vivo exposure to high cholesterol. BMDMs from high cholesterol mice display a heighten M1 and blunted M2-like phenotype. Metabolomic analysis of M(IL-4) macrophages reveal they have breaks in the TCA cycle resulting in reduced capacity to utilise OxPhos which is needed for full M(IL-4) polarisation. Macrophages from chimeric mice generated by bone marrow transfer of high cholesterol bone marrow into irradiated normo-cholesterol mice retain the same phenotype as macrophages from high-cholesterol mice. Critically we demonstrate that there are genome wide irreversible epigenetic changes in bone marrow cells and tissue resident macrophages as a result of exposure to high cholesterol. Mice from a high cholesterol background have an increased number of total HSC (lin-ckit+sca1+) within the bone marrow, however, there is a decreased in the total number of long term (LT)-HSC; critically, this phenotype is not reversible when lipids levels are normalised using monoclonal antibody therapy against PCSK9. This is coupled with an irreversible myeloid skewing in the bone marrow immune cell composition. Newly recruited macrophages within the adipose also retain a heighten M1 and blunted M2-like phenotype despite lipid normalisation conferring a negative systemic metabolic phenotype. Critically, these data show that cholesterol induces long term epigenetic and metabolic changes to HSC and macrophages, which may account for residual inflammatory risk.