The outbreak of Corona Virus Disease-19 (COVID-19), caused by Severe Acute Respiratory Syndrome Corona Virus - 2 (SARS-CoV-2), a global pandemic, is having a significant impact on healthcare, especially the clinical microbiology laboratories all around the world. There are many reports which suggest that the disease can present with gastrointestinal symptoms such as nausea, vomiting, diarrhea, and loss of appetite, which the gastroenterologists may have to deal with. Hence, knowledge about the diagnosis of COVID-19 is important to gastroenterologists as well. The current review therefore covers the challenges faced while choosing appropriate sample collection, transport, and tests for SARS-CoV-2 infection. The right sample at the right time from the right anatomical site with the proper precautions is crucial in prompt and accurate diagnosis of COVID-19. The tests can be divided into direct, indirect, and complementary tests. In the direct test, real-time polymerase chain reaction (RT-PCR) assays are the molecular tests of choice for the diagnosis of COVID-19. Other direct tests include GeneXpert and TrueNAT. In indirect testing, antigen-antibody-based techniques are recommended for surveillance for the disease, which may help to formulate the control measures. Finally, the additional tests help in assessing the disease severity and evaluating the prognosis. All the above tests are important not only for diagnosis but also for management strategy and prognosis.