Paradoxical embolism due to a patent foramen ovale (PFO) is a possible cause of ischemic stroke, particularly in young cryptogenic stroke patients. In most cases, however, it is difficult to establish a firm etiological association and the debate about management is ongoing. The Austrian Paradoxical Cerebral Embolism Trial was designed as a prospective, national, multi-center, non-randomized registry to add further data on this topic before the completion of randomized controlled trials. Over 27 months 188 cryptogenic stroke/TIA patients ≤55 years were entered by 15 Austrian stroke units. Contrast transesophageal echocardiography demonstrated a cardiac right-to-left shunt (RLS) in 176 patients; a pulmonary RLS was assumed in 10, and 2 showed both. Ninety-seven (55 %) patients with cardiac RLS underwent interventional treatment, and this was more likely for patients with stroke as index event, a symptomatic infarction on MRI and a large size of PFO. Over 2 years, recurrences occurred at a rate of approximately 1.3 % for stroke and 4.3 % for TIA, and were especially frequent in patients with pulmonary RLS. When comparing outcomes in patients with cardiac RLS there was a trend for fewer recurrences with interventional management (closure: four TIA in four patients vs. medical: three strokes and seven TIA in nine patients; p = 0.066 for events, p = 0.085 for patients). The complication rate was 13.4, and 5.7 % had residual shunting. The possible causes for paradoxical embolism in young patients with cryptogenic stroke appear more variable than usually considered, and other causes than PFO should not be neglected. Interventional treatment of a cardiac RLS may offer a small benefit, but has to be weighed against possible complications and the problem of establishing causality.