Calibration of a radiation therapy system comprising a radiation unit (10) with a fixed focus point, a fixation unit (50) for fixing a treatment volume in a patient, and a positioning system (20). The positioning system (20) comprises a fixed framework (22), a movable carriage (24) for carrying and moving the entire patient, motor (s), a control system for controlling the motor (s), and at least one engagement point (30, 32) for releasably mounting the fixation unit (50) in fixed engagement with the positioning system (20). A fixation unit coordinate system defined in relation to the fixation unit (50) is provided. Linearity errors for the motional axes of the carriage (24) and the angular offset between the motional axes and the coordinate system is determined, whereby the relationships between the axes of the coordinate system and the motional axes of the positioning system (20) are determined. The positioning system is then mounted in fixed relationship with the radiation therapy unit (10) and the focus point in relation to the positioning system (20) is determined, whereby the relationship between the focus point and the coordinate system is also determined.