The foramen ovale is a slit-like anatomical structure located in the interatrial wall of the fetal heart that enables right-to-left shunting during fetal development. Although this hole generally closes completely shortly after birth due to shifting pressures in the atrial chambers, it remains open, or 'patent', in about 25% of cases representing a potential substrate for right-to-left shunting during adult life. A patent foramen ovale (PFO) is usually haemodynamically insignificant, even when large, but is the most common cause of right-to-left shunt. Large-diameter PFOs may act as a pathway for passage of thrombus, air, fat, vegetation or vasoactive substances from the venous to the arterial circulation, potentially causing paradoxical emboli and stroke, inappropriate decompression sickness in divers, platypnoea-orthodeoxia syndrome and aural migraine. Over the past two decades, the association between PFO and the occurrence of migraine and cryptogenic stroke, particularly in younger adults, has been subject to considerable controversy and debate. Currently, semi-invasive contrast-transoesophageal echocardiography is accepted as the gold standard to detect right-to-left shunt across a PFO, but other imaging modalities utilising contrast such as second-harmonic transthoracic echocardiogram, transcranial Doppler sonography, CT and cardiac MRI have been shown to have similar sensitivity and specificity in detecting a PFO when compared with transoesophageal echocardiography. In this review the authors discuss embryological origins, diagnostic measures and evidence-based treatment options for the prevention of PFO-related paradoxical embolism, with emphasis on cryptogenic stroke and migraine.