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Background and objective Suspicion of an acute allergic reaction is a common reason for attending the emergency department (ED). However, there are few comparisons between the initial diagnosis of suspected allergic reaction made in the ED with the definitive diagnosis made subsequently in the allergy department (AD). Objective: To compare details of the initial diagnosis made in the ED relating to allergy with the final diagnosis made in the AD. Methods Patients attending the ED of 2 hospitals with suspected allergic reactions were prospectively enrolled based on key words. A certified allergy specialist reviewed the ED records of these patients and, if these were suggestive of an allergic reaction, the patients were scheduled for further evaluation at the allergy clinic. Results In total, 2000 patients were enrolled between April 2013 and October 2015. Of these, 1333 passed the initial assessment and underwent further evaluation. Of the 1333 patients, 528 underwent an allergological study, and 206 were confirmed as being allergic. With respect to drug allergy, nonsteroidal anti-inflammatory drugs were the most common triggers, followed by β-lactams; in food allergy, plant-based foods were the most common. Only 16.4% of patients confirmed as having anaphylaxis in the AD were initially diagnosed with the condition in the ED. Conclusion Of the 528 patients who finally underwent the full allergological study, fewer than half were confirmed as allergic. Moreover, anaphylaxis appears to be underdiagnosed in the ED. Better communication between the ED and the AD is necessary to improve the diagnosis and management of these patients.