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We report two cases of paradoxical cerebral embolism in adults with congenital heart disease (ACHD) with residual atrial shunt lesions, a 59 year-old male patient with partial detachment of a surgical ASD closure patch, and a 57 year-old male patient with Ebstein’s anomaly and a large patent foramen ovale. Considering these mechanisms and the increasing incidence of venous thrombosis with age, a higher prevalence of paradoxical embolism in ACHD patients with residual atrial shunts may be suspected. Regular follow-up of patients with ACHD remains important throughout life even in seemingly stable lesions.