Intrafractional organ motion remains a source of error in conformal radiotherapy of dynamic targets such as tumours of the lung or of the prostate. The purpose of this work was to devise a method for the continuous and routine measurement of intrafractional organ motion. The method consists of a combination of an electromagnetic (EM), internal marker-based tracking system with the on-board kilovoltage x-ray imaging system of a modern treatment machine. The EM system continuously tracks the target, while x-ray images can be acquired simultaneously if demand arises. An image processing algorithm has been developed to automatically localize and track the EM markers in the x-ray images. We have demonstrated simultaneous target tracking using the EM system and x-ray imaging of a mobile target inside a programmable thorax phantom. The target motion was very well reproduced by both systems. The comparability of the target locations reported by both systems was established (better than 0.25 mm up to target velocities of 3 cm s(-1)). One immediate use of the synchronized system was shown: the generation of a 4D cone beam computed tomography data set using the EM system for the measurement of motion. In conclusion, we have developed a system for the routine measurement of intrafractional motion that continuously provides the 3D position of the target with the ability to acquire images of the treatment field only when needed, thereby eliminating avoidable imaging dose to the patient.