The increased prevalence of opioid use disorder (OUD) has made it imperative to disentangle the biological mechanisms contributing to individual differences in susceptibility to OUD. OUD shows strong heritability, however genetic variants contributing toward vulnerability remain poorly defined. We performed a genome-wide association study (GWAS) using over 850 male and female heterogeneous stock rats to identify genes underlying behaviors associated with OUD such as analgesia, as well as heroin-taking, refraining and seeking behaviors. By using an animal model of OUD, we were able to identify genetic variants associated with distinct OUD behaviors while maintaining a uniform environment, an experimental design not easily achieved in humans. Furthermore, we applied an animal model capturing individual variation in OUD propensity to assess if GWAS results were associated with OUD vulnerable versus resilient behavioral phenotypes. Our findings confirm the heritability of several OUD-like behaviors, including overall phenotype. We identified several genetic variants associated with basal analgesia prior to heroin experience, heroin consumption, escalation of intake, and motivation to obtain heroin. Ets2 , a regulator of microglia functional plasticity, and its eQTL PCP4 were identified for heroin consumption, and were associated with an OUD vulnerable phenotype through phenotype wide association study analysis. Furthermore, the coding variant Phd1l2 and the eQTL MMP15 for break point are both known mediators of addiction-related behaviors, and correlated with OUD vulnerability. These findings identify novel genetic markers related to individual differences in the susceptibility to OUD-relevant behaviors.