Introduction: Accurate provisional diagnosis in the Emergency Department (ED) is important as it has a significant impact on safety. It also affects the patients’ treatment, length of stay and cost of treatment. The data on the accuracy of making diagnosis made by ED doctors is scarce and most results vary with different countries. This study was conducted to evaluate the accuracy of the diagnosis made by the ED doctors in Hospital Universiti Sains Malaysia (USM) and the factors contributed to the discrepancy. Method: This was a retrospective cross-sectional study conducted in Hospital USM from May 2016 to December 2017. Medical records of the patients who were admitted to the hospital were selected using simple random sampling methods. The folders were reviewed and the association within the categorised diagnosis accuracy was analysed using the ICD-10 classification. The sample size was 180 cases, and cases were divided into two main categories. The factors associated with the unmatched diagnosis from both patients and provider were then measured using multiple logistic regressions. Results: Hospital USM Emergency Department had 15.6 per cent of unmatched diagnosis and 84.4 per cent of matched diagnosis. No difference between age and gender in making accurate diagnosis. The odds of having unmatched diagnosis in patients from the green zone are 4.2 times higher compared to the red zone. Conclusion: ED Hospital USM has a high diagnostic accuracy, especially involving the patients in red zone and yellow zone.