The clinical implications of patent foramen ovale (PFO) morphology are still debated. Quantitative analysis by transesophageal echocardiography (TEE) is helpful in characterizing PFO morphology. The aim of this study was to determine whether there were differences in the anatomy of PFOs on TEE in patients with and without recurrent cryptogenic stroke or transient ischemic attack. The results of TEE in 58 patients who had PFO closure for cryptogenic cerebrovascular accident (CVA) were compared with those in 58 consecutive asymptomatic patients with PFOs found incidentally on TEE. The data were analyzed for differences in PFO size (maximum separation of the septum primum and septum secundum), tunnel length (maximum overlap of the septum primum and septum secundum), the presence of atrial septal aneurysm (>11 mm mobility), the severity of shunting (mild, 3 to 9 microbubbles; moderate, 10 to 30 microbubbles; severe, >30 microbubbles), the prominence of the Eustachian valve; and the presence of Chiari's network. Patients with CVAs had larger PFOs (3.9 +/- 1.6 vs 2.9 +/- 1.4 mm, p <0.001), longer tunnels (14 +/- 6 vs 12 +/- 6 mm, p = 0.05), and a greater frequency of atrial septal aneurysm (45% vs 21%, p <0.005) compared with controls. They also had a greater proportion of large (>or=4 mm) PFOs (46% vs 17%, p <0.001), long (>or=1 cm) tunnels (78% vs 55%, p <0.01), and severe shunting (16% vs 5%, p <0.06). The frequencies of prominent Eustachian valves and Chiari's network were not significantly different. In conclusion, PFOs in patients with cryptogenic CVAs are larger, have longer tunnels, and are more frequently associated with atrial septal aneurysms. This information should be considered when evaluating patients with cryptogenic CVAs.