A system for treating a target area in a patient with an irradiation beam, comprising: (a) a tracking assembly configured to track the position of a patient body region containing the target area and at least one radiation-sensitive area with respect to a known reference axis in an external coordinate system; (b) a beam source configured to direct a collimated X-ray beam at the patient target area along a known beam axis (1400, 1400a, 1400b, 1400c) to intersect with a known treatment axis (19, 2820) defined with respect to the reference axis (18, 2810) in the external coordinate system; and (c) a processor (106, 501) operatively connected to the tracking device and beam source, and configured to: (i) determine, from the known position of body region in the external coordinate system, the coordinates of the target area to be treated and the coordinates of the at least one radiation-sensitive patient structure; (ii) during a period when the beam is being directed along the known beam axis to intersect with the known treatment axis at the target area, and based on information received from the tracking device, track the positions of the target area to be treated and the at least one radiation-sensitive structure; (iii) based on the known beam axis of the collimated beam in the external coordinate system, and the instantaneous positions of the target area to be treated and the at least one radiation-sensitive structure, calculate a total radiation equivalent received at the target area and at least one radiation-sensitive structure; and (iv) based on the calculated radiation equivalents from step (iii), control the irradiation beam to ensure that the at least one radiation-sensitive structure does not receive more than a preselected radiation equivalent during the treatment. (a) a tracking assembly configured to track the position of a patient body region containing the target area and at least one radiation-sensitive area with respect to a known reference axis in an external coordinate system; (b) a beam source configured to direct a collimated X-ray beam at the patient target area along a known beam axis (1400, 1400a, 1400b, 1400c) to intersect with a known treatment axis (19, 2820) defined with respect to the reference axis (18, 2810) in the external coordinate system; and (c) a processor (106, 501) operatively connected to the tracking device and beam source, and configured to: (i) determine, from the known position of body region in the external coordinate system, the coordinates of the target area to be treated and the coordinates of the at least one radiation-sensitive patient structure; (ii) during a period when the beam is being directed along the known beam axis to intersect with the known treatment axis at the target area, and based on information received from the tracking device, track the positions of the target area to be treated and the at least one radiation-sensitive structure; (iii) based on the known beam axis of the collimated beam in the external coordinate system, and the instantaneous positions of the target area to be treated and the at least one radiation-sensitive structure, calculate a total radiation equivalent received at the target area and at least one radiation-sensitive structure; and (iv) based on the calculated radiation equivalents from step (iii), control the irradiation beam to ensure that the at least one radiation-sensitive structure does not receive more than a preselected radiation equivalent during the treatment. (i) determine, from the known position of body region in the external coordinate system, the coordinates of the target area to be treated and the coordinates of the at least one radiation-sensitive patient structure; (ii) during a period when the beam is being directed along the known beam axis to intersect with the known treatment axis at the target area, and based on information received from the tracking device, track the positions of the target area to be treated and the at least one radiation-sensitive structure; (iii) based on the known beam axis of the collimated beam in the external coordinate system, and the instantaneous positions of the target area to be treated and the at least one radiation-sensitive structure, calculate a total radiation equivalent received at the target area and at least one radiation-sensitive structure; and (iv) based on the calculated radiation equivalents from step (iii), control the irradiation beam to ensure that the at least one radiation-sensitive structure does not receive more than a preselected radiation equivalent during the treatment.