This report describes a case of isthmus-dependent atrial flutter ablation by the femoral approach in a 77-year-old patient with a previously unknown absence of the inferior vena cava (IVC). Multi-row detector CT angiography indicated the absence of the perihepatic IVC, whereas the venous blood is drained into the superior vena cava (SVC) via the vena azygos. An ablation catheter could be advanced through the right femoral vein reaching the right heart via vena azygos and SVC. Despite looping of the catheter, ablation and termination of atrial flutter were performed successfully. This is the first report of an inferior-to-superior approach for ablation of atrial flutter in the absence of the perihepatic IVC.