Electromagnetic tracking potentially may be used to guide percutaneous needle-based interventional procedures. This brief report describes our initial experience with an electromagnetic guidance system featuring real-time tracking of respiratory-related target motion using an internal fiducial. An algorithm based on a “freehand” needle puncture technique was employed to puncture the right portal vein and a right hepatic vein for percutaneous intrahepatic portosystemic shunt in a swine model. Preoperative computed tomographic images registered with the electromagnetically tracked needle position were displayed for guidance. Successful puncture was confirmed angiographically. Simultaneous percutaneous transhepatic puncture of the targeted veins was accomplished on the initial attempt.