Background: Detailed anatomic variants of the interatrial septum in patients with right-to-left shunt and contribution of specific anatomies to the risk of ischaemic recurrences has not yet been comprehensively classified. Objective: To report a classification of the anatomic variants of the interatrial septum as observed by intracardiac echocardiography and its correlation with clinical and functional characteristics. Methods: We retrospectively reviewed the medical and instrumental data of 520 consecutive patients (mean age 44±15. 5 years, 355 women) who had over a 10-year period undergone intracardiac echocardiography and right-to-left shunt catheter-based closure. The four main features used to analyse were: (a) diameter of the oval fossa, (b) presence and length of the channel, (c) presence and degree of atrial septal aneurysm, and (d) rim thickness. The presence of Eustachian valve was also tabulated. Results: The combinations of interatrial septum anatomical features were classified into six main anatomical subgroups. Recurrent embolism, multiple ischaemic foci on brain magnetic resonance imaging, high grade shunt, and permanent shunt before transcatheter closure procedure were associated with type 2, type 4, and type 6. Type 4 anatomical subtype (OR 4.1, 1.5–8 [95% CI], p<0.001) and type 2+presence of Eustachian valve (OR 4.3, 1.6–9 [95% CI], p<0.001) were the strongest predictors of recurrent ischaemic events before transcatheter closure. Conclusion: Our study showed that interatrial septum anatomy greatly differs among patients with right-to-left shunt, as well as the risk of ischaemic recurrences in different anatomies.