Background: Some thrombophilic patients have been excluded from clinical trials of septal defect closure due to the presumed higher risk of thrombus formation. The purpose of this study was to assess whether pre-existing thrombophilia predisposes patients to adverse events after percutaneous patent foramen ovale (PFO) or atrial septal defect (ASD) closure. Methods: A retrospective observational study was performed including 147 patients with thrombophilia who were referred for percutaneous PFO or ASD closure for cryptogenic stroke or transient ischemic attack (n = 104, 70.7%), migraine (n = 30, 20.4%), peripheral embolism (n = 5, 3.4%), right ventricular enlargement (n = 2, 1.4%), desaturation (n = 1, 0.7%), or a combination of diagnoses (n = 4, 2.7%). Post-procedure follow-up included 3-6 month clinical evaluation, chart review, or phone call. Results: Of the 147 patients (46 ± 13 years of age, follow-up of 43.5 ± 34.7 months) who met the inclusion criteria, 142 had a PFO (96.6%), and 5 had an ASD (3.4%); 69 (46.9%) underwent closure. Of the closure patients, 1 (1.4%) developed thrombus (Amplatzer ASO device). There were no cases of endocarditis or device erosion. One patient had a stroke post-closure (1.4%). Of the 80 women with stroke, TIA, or peripheral arterial embolism, 52 (65.0%) were taking oral contraceptive pills or hormone replacement therapy at the time of the event.