Introduction Patients with substance use disorders (SUDs) frequently seek emergency care, and the emergency department (ED) may be their only point of contact with the healthcare system. While the ED visit has been increasingly recognized as providing opportunity for interventions around substance use, many questions remain. Methods In December 2016 the Coalition on Psychiatric Emergencies (CPE) convened the first Research Consensus Conference on Acute Mental Illness, which consisted of clinical researchers, clinicians from emergency medicine, emergency psychiatry, emergency psychology, representatives from governmental agencies and patient advocacy groups. Background literature review was conducted prior to the meeting, and questions were iteratively focused, revised, voted on and ranked by perceived importance using nominal group method. Results The main goal of the SUD workgroup was to identify research priorities and develop a research agenda to improve the early identification of and management of emergency department (ED) patients with SUDs with the goal of improving outcomes. This article is the product of a breakout session on “Special Populations: Substance Use Disorder.” The workgroup identified with high consensus six research priorities for their importance related to the care of ED patients with SUDs in these overall domains: screening; ED interventions; the role of peer navigators; initiation of SUD management in the ED; specific patient populations that may impact the effectiveness of interventions including sociogenerational and cultural factors; and the management of the acutely intoxicated patient. Conclusion Emergency providers are increasingly recognizing the important role of the ED in reducing adverse outcomes associated with untreated SUDs. Additional research is required to close identified knowledge gaps and improve care of ED patients with SUD.