Our study aimed to evaluate the diagnostic accuracy of MR versus CT for identifying the etiology of abdominal pain in emergency department patients. This is a prospective study that included patients ≥12-years-old who were being evaluated for possible appendicitis. All patients underwent both MR and CT; images were interpreted by three radiologists who were blind to the patient’s outcome. There were 113 instances of acute abdominal processes (15 different diagnoses). The overall accuracy of NC-MR, CE-MR, and CT was 77%, 83%, and 90% for individual reads and 82%, 84%, and 94% for consensus reads.