Background: Understanding the prevalence of substance use disorder (SUD) in emergency department (ED) settings could facilitate prevention and treatment responses to the epidemic. However, little information is available on the true prevalence of SUD in the ED population. We characterized 1) methods for determining the prevalence of substance use and SUDs within an ED, and 2) the degree to which prevalence differs between geographically proximate EDs. Methods: This cross-sectional, multi-hospital study analyzed data from prior studies and electronic health records (EHR). Our data sources included 1) interviews of a population-based sample of ED patients, 2) chart review for a cohort of ED patients, and 3) ICD-9 codes from an urban, academic trauma center. In addition, ICD-9 codes were obtained for three geographically proximate hospitals of differing type. The sampling methods and ED settings were compared descriptively in terms of their population characteristics and estimated prevalence of SUDs. Results: Prevalence of SUDs at the urban academic center was extremely high, particularly when measured by prospective survey, but also with chart review. Use over the prior year (binge drinking, illicit drug use, or treatment for alcohol or drug use) as determined by self-report and chart review respectively was: 41.9% and 15.2% for alcohol, 36.2% and 21.6% for drugs, and 59.2% and 30.4% for either. Estimates using ICD-9 codes indicated a far lower prevalence of substance use and suggest differences between EDs. Conclusions: SUDs are highly prevalent in ED populations, though significant variability between EDs is likely. SUDs are infrequently coded, suggesting that clinicians may be unaware of SUDs, or that discharge coding is insufficient to understand and respond to SUDs. Feasible and efficacious methods of identification and documentation of SUDs is an urgent priority to aid efforts to facilitate health services planning and quality improvement, and enable pragmatic clinical trials.