This study examined the relationship between electronic medical records (EMR) sophistication and the efficiency of U.S. hospital emergency departments (EDs). Using data from the 2006 National Hospital Ambulatory Medical Care Survey, survey-weighted ordinary least squares regressions were used to estimate the association of EMR sophistication with ED throughput and probability a patient left without treatment. Instrumental variables were used to test for the presence of endogeneity and reverse causality. Greater EMR sophistication had a mixed association with ED efficiency. Relative to EDs with minimal or no EMR, fully functional EMR was associated with 22.4% lower ED length of stay and 13.1% lower diagnosis/treatment time. However, the relationships varied by patient acuity level and diagnostic services provided. Surprisingly, EDs with basic EMR were not more efficient on average, and basic EMR had a nonlinear relationship with efficiency that varied with the number of EMR functions used.