Strokes that remain without a definite cause even after extensive work-up are classified as cryptogenic. These constitute about 30-40% of all strokes. Stroke aetiology may remain undetermined for the following reasons: (i) the cause of stroke is transitory or reversible and the diagnostic work-out is not therefore performed at the appropriate time; (ii) all known causes of stroke are not fully investigated; (iii) some causes of stroke remain unknown. Recent studies have challenged the previous view that cryptogenic stroke is a relatively benign cerebrovascular event, and have shown that cryptogenic stroke is associated with a higher rate of recurrence and adverse outcome at long-term follow-up. The determination of stroke aetiology is a valuable procedure to avoid the risk of stroke recurrence, especially in young patients. In this review, we discuss new evidence on the aetiology of cryptogenic stroke, specifically focusing on patients with patent foramen ovale and atheroma of the aortic arch.