For calibrating a multi-plane X-ray unit, an internal matrix mapping coordinate system internal to the unit onto coordinate system of a first radiographic plane is predefined in a reference projection geometry. An external matrix mapping coordinate system external to the unit onto coordinate system of the first plane is determined from image data captured by the first plane at calibration points and coordinates of the calibration points. An external matrix mapping coordinate system external to the unit onto coordinate system of a second radiographic plane is determined from image data captured by the second plane at the calibration points and the coordinates of the calibration points. A measure of position of the second plane with respect to coordinate system internal to the unit or with respect to the first plane is determined from the internal and external matrix of the first plane and the external matrix of the second plane.