Abstract: Background: The transesophageal echocardiogram (TEE) is the standard imaging modality for confirming the presence or absence of patent foramen ovale. There is a causal association between PFO and unexplained stroke. It seems that 3D-TEE can present a high-risk PFO morphological feature, which seems to show more than just being easier to open. Methods: In total 134 consecutive patients with cryptogenic stroke or migraine who had suspected PFO and underwent c-TCD, TTE, and c-TEE were included in this study. TEE confirmed the PFO. The right-to-left shunt (RLS) grade of PFO at rest and abdominal compression Valsalva maneuver was detected by c-TEE. Results: The long diameter of FO (1.74±0.3 vs. 1.60±0.4, P=0.039), the short diameter of FO (1.12±0.3 vs. 1.00±0.3, P=0.036), perimeter of FO (4.62±0.7 vs. 4.22±1.0, P=0.026) and area (1.80±0.8 vs. 1.35±0.8, P=0.05) of the FO were significantly larger in the larger RLS group. The cut-off value calculated by ROC for the diagnosis of high-risk PFO was that the length of the PFO tunnel was 12 mm and Left funnelform combined with multiple exits of left atrial (sensitivity was 92%, specificity was 90%). Conclusions: A larger oval fossa can be more easily activated and cause a large right-to-left shunt. The left funnelform, a longer length of the PFO tunnel, and multiple exits of the tunnel of LA increase the risk of CS in anatomical of PFO respect. TEE can precisely visualize the specific morphological characteristics of PFO. These features on TEE have a strong correlation with CS.