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Abstract Background Portsmann and co. performed the first PDA device closure in 1967. The technique and the devices used have evolved since then and are the first choice in managing anatomically feasible patent ductus arteriosus (PDA) for the last 20 years. Though catheter-based closure of PDA is generally a simple procedure, there are instances when the interventionist faces challenges, especially in smaller children, with syndromic features and venous anomalies even when defects are small and pulmonary artery pressures are normal. Although the femoral vein is the relatively risk-free standard access, internal jugular vein, femoral artery, and transhepatic IVC can be used to close the PDA in different anomalies. The rare venous anomaly of infrahepatic interruption of the IVC with azygous continuation poses technical challenges when percutaneous closure of PDA was attempted through the standard femoral access. Case presentation We report a rare case of PDA device closure in a syndromic child with a short neck having interrupted IVC via femoral-azygous venous approach. Conclusion Knowledge of the IVC course and its anomalies should be known to the operator before the percutaneous closure of PDA. Although other approaches are available, femoral vein approach can be used in case of interrupted IVC for percutaneous closure of PDA.