Acute upper respiratory infections (URIs) represent a major source of annual emergency department (EDs) visits in the United States. However, the definitive etiology of symptoms is generally not determined as testing has historically been prioritized for influenza virus and recently, respiratory syncytial virus (RSV). To elucidate the prevalence, rates of co-infections, and etiologic composition of URIs from symptomatic adult ED patients, we evaluated specimens from four geographically diverse EDs in the United States from 2013-2014 utilizing a multiplex molecular diagnostic assay. 1941 ED patients who had signs and/or symptoms of an acute URI and were considered ‘high-risk’ for influenza related complications according to CDC criteria, were consecutively enrolled and tested for influenza; influenza prevalence was 9.4% (183/1941). Among them, 799 nasopharyngeal swab specimens with sufficient residual volumes were subsequently tested for additional respiratory pathogens. The overall positivity rate was 30.1% (241/799), of which 6.6% (16/241) were co-infected. Non-influenza pathogens from most to least common were: rhinovirus/enterovirus, coronavirus, human metapneumovirus and RSV, respectively. The ratio of co-infection to mono-infection was highest amongst those with adenovirus, versus mon-infections (2.0). Broad differences in disease prevalence and pathogen distributions were observed across geographic regions; the site with the highest detection rate (for both mono and co-infections) demonstrated the greatest pathogen diversity. Adult ED patients at high-risk for influenza complications were infected with a variety of respiratory pathogens and geographic variations in the disease prevalence and co-pathogen type were observed. Further research is required to evaluate the clinical relevance of these findings.