A 25-year-old woman presented with Streptococcus milleri brain abscess. Previous cardiac history was unremarkable. In search for a source of embolism echocardiography was performed and revealed a previous undiagnosed Ebstein's anomaly of moderate severity with apical displacement of the septal leaflet of the tricuspid valve and a secundum atrial septal defect (ASD) with left to right shunt. The combination of increased right atrial pressure caused by Ebstein's and an ASD with possibility of transient right to left shunt predispose for paradoxical embolization. The most likely reason for development of a brain abscess in this patient is septic embolization from an infectious focus outside the heart. Ebstein's anomaly can remain undiagnosed until adulthood if the right ventricle, in spite of the smaller size, is haemodynamically well functioning.