Antiphospholipid syndrome (APS) is characterised by thrombosis (which may be venous, arterial, or microvascular) and/or pregnancy morbidity, in association with persistently positive antiphospholipid antibodies (aPLs). Although thrombosis and pregnancy morbidity are the main clinical criteria for a diagnosis of APS in the revised Sapporo (Sydney) criteria, recently published American College of Rheumatology (ACR)/European Alliance of Associations for Rheumatology (EULAR) classification criteria for APS have significantly refined the diagnostic algorithm to include a scoring system clustered into 6 clinical domains (macrovascular venous thromboembolism, macrovascular arterial thrombosis, microvascular thrombosis, obstetric, cardiac valve, and hematologic). Diagnosis of APS is complicated by the fact that significant heterogeneity exists in patients’ clinical presentation, underlying vascular risk factors and methods of detecting aPL. Despite the autoimmune nature of APS, anticoagulation remains the main strategy for secondary prevention of thrombosis. However, optimal antithrombotic treatment in APS patients with arterial thrombosis remains controversial due to a paucity of data from randomised controlled studies. In this paper, we present two cases and highlight the diagnostic and therapeutic challenges they pose and how we approach them in the light of current evidence.