BACKGROUND: The diagnosis of COVID-19 is made by detection of SARS-CoV-2 RNA by reverse transcription polymerase chain reaction (RT-PCR). Studies have shown a percentage of up to 30 % false negative results. CASE PRESENTATION: A previously healthy man in his late thirties was admitted to the hospital after 3-5 days of suffering chest pain, dyspnoea and abdominal discomfort. He had hypoxic respiratory failure and required oxygen therapy. The routine nasopharyngeal swab for PCR was negative at days 5 and 7 after onset of symptoms. A specimen obtained from bronchoalveolar lavage on day 8 was positive. INTERPRETATION: This case report shows us that even in the early course of SARS-Cov-2 infection, when the viral load in the upper respiratory tract has been shown to be at its highest, there might be false negative tests. It also emphasises the importance of including other clinical measures before discontinuation of isolation.