The invention is related to a method and a magnetic resonance tomography unit for tracking a medical instrument. A tracking volume is defined enclosing a predefined trajectory of the medical instrument. 2D projection images of the tracking volume in presence of the medical instrument are acquired with the magnetic resonance tomography unit from two different view angles. Reference 2D images for the two view angles are determined and a background of the 2D projection images is suppressed. Two sets of 2D coordinates of the medical instrument are extracted from the two 2D projection images and combined to a 3D coordinate set and output on a display.