Epigenetic modifications, including DNA methylation and microRNAs, play an important role in modulating the risk for opioid use disorder and in mediating the consequences of this illness. Opioid exposure can cause lasting changes in brain gene expression, partially via epigenetic mechanisms. An integrated analysis of the different levels of epigenetic regulation of gene expression is needed to completely understand the mechanisms of neurotoxic effects in opioid use disorder. This chapter will discuss multi-omics approaches and recent genome-wide findings of epigenetic modifications in human postmortem brain of patients with opioid use disorder, including data integration and analyses across different molecular layers that allow cross-validation of gene network modulations, and highlight neurovascular alterations as a consequence of opioid exposure. Elucidation of the epigenetic mechanisms of opioid-induced brain alterations may lead to identification of targets for novel treatments that could alter disease course or reduce the severity of complications induced by these drugs.