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Background: Closure of patent ductus arteriosus (PDA), ventricular septal defect (VSD) and atrial septal defect (ASD) can be done surgically or by device. This study was designed to compare the total cost of surgical or device closures of PDA, ASD or VSD for Iranian patients. Methods: This is a cross-sectional study, conducted from January 1, 2005 until January 1, 2006 in two large heart centers of Tehran. The study population consisted of 91 patients with isolated PDA, ASD or VSD who underwent either surgical or device closure.   Results: PDA device closure either with the Amplatzer device or coil was less costly than that via surgery. VSD closure with the Amplatzer device was more costly (17.6%). Although ASD closure was also more expensive (15.4%), the difference was not statistically significant. Conclusion: It can be concluded that PDA closure is cheaper than surgery in Iran. ASD and VSD device closures are more expensive, but the added cost can be affordable in view of the advantages of device closure.