Abstract. Electromagnetic tracking is currently the only available technology to track flexible instruments inside the human body without the use of real time imaging technology such as ultrasound or mobile c-arms. The limitation of electromagnetic tracking is its accuracy and sensibility to the environment, especially in the presences of ferromagnetic material and electronic devices. Navigation systems based on these technologies were recently introduced especially flexible endoscopy. One design goal for setting up such navigation systems is the removal of all material from the close environment that can perturb the magnetic field. In our scenario, within the radiation therapy room, we can not eliminate the gantry. Thus, existing methods for electromagnetic tracking error estimation and correction algorithms were reviewed, implemented, and adopted to the special requirement for navigation during prostate cancer treatment.