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Popliteal venous aneurysm (PVA) and antiphospholipid syndrome (APS) are under-recognised as potential causes of pulmonary embolism (PE). A 66-year-old woman presented with progressive shortness of breath. A contrast-enhanced CT revealed bilateral PE, a small renal infarction and bilateral PVAs. Direct oral anticoagulant (DOAC) therapy was initiated immediately for venous thrombosis. Given the positivity for serum antiphospholipid antibody (aPL) in an initial blood test, low-dose aspirin was included to prevent further arterial thrombosis. Her symptoms resolved and she was discharged 1 week later. Twelve weeks later, she was diagnosed with APS because of persistent aPL. Surgical resection of the right PVA was performed 1 year later from her hospitalisation. To the best of our knowledge, this is the first case of PE caused by the combination of bilateral PVAs and APS. This report emphasises the importance of careful screening to identify PE causes, and its optimal management.