Background: Percutaneous closure devices for cardiac defects have been used with a high degree of efficacy and safety. However, patients with autoimmune disease or immunosuppression are excluded in clinical trials due to their presumed higher risk. Percutaneous closure of patent foramen ovale (PFO) or atrial septal defect (ASD) is safe in patients who are immunosuppressed or have autoimmune disease. Methods: A retrospective observational multicenter study was performed including 24 patients who were immunocompromised or had autoimmune disease from vasculitis, Human Immunodeficiency Virus, hepatitis, cancer, or renal transplant and underwent percutaneous PFO or ASD closure for cryptogenic stroke (9.38%), desaturation (5.21%), migraine (7.29%), or a combination of these diagnoses (3.13%). Post-procedure follow-up included clinical evaluation at 3-6 months or telephone questionnaire up to 8 years later. Results: Of the 24 patients who met inclusion criteria (53 ± 14 years of age, follow-up of 21 ± 28 months), 19 had a PFO (79%), 5 had an ASD (21%), and 21 (88%) underwent closure. There was no evidence of endocarditis, device erosion, exacerbation of migraine, or recurrent stroke. Only one patient (4%) experienced a transient neurologic deficit after closure due to complex migraine with visual aura. Mortality status, which was verified by the social security death index, showed five deaths related to non-cardiac conditions. Conclusion: This observational study of an uncommon condition suggests that percutaneous closure of a PFO or ASD is safe in immunocompromised patients.