There is increasing evidence that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection causes an unusual pneumonia and a pro-coagulant state that significantly increases the risk of arterial and venous thromboembolism. We hypothesize that, in select patients, some complications of COVID-19 may be due to right-to-left (RTL) shunt. Shunt may be intra-pulmonary, or extra-pulmonary, and can cause paradoxical embolization, hypoxia and platypnoea orthodeoxia. Saline microbubble contrast echocardiography is a minimally invasive, inexpensive, bedside test that can detect, quantify, and define the anatomical substrate of intra-pulmonary and intra-cardiac shunts. The prevalence of patent foramen ovale (PFO) in the general population is high (20–30%) but is even higher in patients who have a stroke (50%). Thus, the striking absence of data on patients with PFO who develop COVID-19 suggests that this is being under-diagnosed. This may be because physicians and sonographers currently feel that screening for shunt is unnecessary. This could be an unintended consequence of guidance from several specialist societies to defer procedures to close PFO until after the pandemic. This may be counterproductive. Patients with shunt may be at particularly high risk of complications from COVID-19 and interventions to minimise RTL shunt could prevent paradoxical embolization and improve hypoxia in select high risk patients with COVID-19.