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Bronchoscopy, as an aerosol-generating procedure, is not routinely performed in patients with high-risk of coronavirus disease-2019 (COVID-19) owing to potential transmission to healthcare workers. However, to obtain lower respiratory specimens from bronchoscopy with bronchoalveolar lavage (BAL) is necessary to confirm COVID-19 or other diagnosis that will change clinical management. We report a case of diagnostic difficulty with five negative SARS-CoV-2 RT-PCR testing in four upper respiratory tract and one stool samples following presentation with fever during the quarantine period and a strong epidemiological linkage to an index patient with COVID-19. The final diagnosis was confirmed by BAL. Special precautions to be taken when performing bronchoscopy in high-risk non-intubated patients were discussed.