A method of aligning the radiation beam in a radiotherapy system comprising a source for producing a beam of radiation and an imaging device for imaging from the beam, both mounted to be rotatable about an axis, a fiducial phantom between the source and imaging device, the method comprising: rotating the beam and imaging device in a trajectory about the axis while obtaining images of the fiducial phantom from a plurality of different angles, at least one image including a feature of the imaging apparatus, adjusting the trajectory of the source relative to that feature to position the isocenter substantially in the center of the volume, determining from each image of the fiducial phantom the position of the source at the rotational position the image was obtained, and calculating the center of rotation of the positions of the source to define the isocenter of the system.