Systems and methods for tracking targets in real time for radiation therapy and other applications. In one embodiment, a method includes collecting position information of a marker implanted within a patient at a site relative to the target at a time tn, and providing an objective output indicative of the location of the target based on the position information collected at time tn. The objective output is provided to a memory device, user interface, and/or radiation delivery machine within 1 ms to 2 seconds of the time tn when the position information was collected. This embodiment of the method can further include providing the objective output at a periodicity of 10-200 ms during at least a portion of a treatment procedure. For example, the method can further include generating a beam of ionizing radiation and directing the beam to a machine isocenter, and continuously repeating the collecting procedure and the providing procedure every 10-200 ms while irradiating the patient with the ionizing radiation beam.
