The increased prevalence of opioid use disorder (OUD) world-wide has made it imperative to disentangle the biological mechanisms contributing to OUD propensity. OUD shows strong heritability, however genetic variants contributing toward vulnerability remain under explored. In the current study, genome-wide association (GWAS) analysis on over 850 male and female heterogeneous stock rats were performed to identify genes underlying heroin-taking, refraining and seeking behaviors. By using an animal model of OUD, we were able to identify genetic variants associated with distinct behaviors contributing to OUD, an experimental design not easily achieved in human GWAS analysis, and not performed to date for OUD GWAS studies. Our findings show, akin to the human population, several heritable traits related with OUD. We also identified genetic variants associated with heroin consumption, escalation of intake, motivation to obtain heroin, and basal levels of analgesic threshold prior to heroin experience, which was behaviorally unrelated to the heroin behaviors. Several of the genes identified are known biomarkers of other substance use disorders and mediators of neurobiological mechanisms underlying addiction-related behaviors. These findings emphasize the need to assess the role of these genetic variants in OUD, thereby augmenting our understanding of risk factors and neurobiological processes associated with OUD vulnerability.