The correlation between atrial septum anatomy and the risk of ischemic neurological events remains underexplored. This study aimed to examine both the functional and anatomical attributes of the atrial septum and identify predictors of stroke and/or transient ischemic attack (TIA) in patients diagnosed with patent foramen ovale (PFO). A total of 155 patients diagnosed with PFO, with a cardiological cause of neurological events, were enrolled. Transesophageal echocardiography was utilized to assess the anatomy of the PFO canal, size of the right-to-left shunt, thickness of the primary and secondary atrial septum, presence of atrial septum aneurysm, and anatomical structures of the right atrium. Regression analysis showed that factors such as female sex, hypercholesterolemia, PFO canal width, and a large right-to-left shunt were significantly associated with stroke and/or TIA. Receiver operating characteristic analysis indicated that the width of the PFO canal holds a relatively weak, although significant predictive, value for ischemic neurological episodes (area under the curve = 0.7; P = 0.002). A PFO canal width of 4 mm was associated with 70% sensitivity and 55% specificity for predicting stroke and/or TIA. The atrial septum's anatomy, especially the dimensions of the PFO canal and the magnitude of the right-to-left shunt, combined with specific demographic and clinical factors, are linked to ischemic neurological incidents in PFO patients.