International rates of hospitalization for atrial fibrillation and flutter (AFF) from the emergency department (ED) vary widely without clear evidence to guide the identification of high-risk patients requiring inpatient management. We sought to determine (1) variation in hospital admission and (2) modifiable factors associated with hospitalization of AFF patients within a U.S. integrated health system. This multicenter prospective observational study of health plan members with symptomatic AFF was conducted using convenience sampling in 7 urban community EDs from 05/2011 to 08/2012. Prospective data collection included presenting symptoms, characteristics of atrial dysrhythmia, ED physician impression of hemodynamic instability, comorbid diagnoses, ED management, and ED discharge rhythm. All centers had full-time on-call cardiology consultation available. Additional variables were extracted from the electronic health record. We identified factors associated with hospitalization and included predictors in a multivariate Poisson Generalized Estimating Equations regression model to estimate adjusted relative risks while accounting for clustering by physician. Among 1,942 eligible AFF patients, 1,074 (55.3%) were discharged home and 868 (44.7%) were hospitalized. Hospitalization rates ranged from 37.4% to 60.4% across medical centers. After adjustment, modifiable factors associated with increased hospital admission from the ED included non-sinus rhythm at ED discharge, no attempted cardioversion, and heart rate reduction. Within an integrated health system, we found significant variation in AFF hospitalization rates and identified several modifiable factors associated with hospital admission. Standardizing treatment goals that specifically address best practices for ED rate reduction and rhythm control may reduce hospitalizations.