A method and system for providing intensity modulated radiation therapy to a moving target is disclosed. According to a preferred embodiment of the invention, a treatment plan for providing radiotherapy using a multi-leaf collimator (“MLC”) comprises a plurality of sub-plans, each of which is optimized for a different phase of target movement. Movements of the treatment target are tracked in real time, and the choice of which sub-plan to implement is made in real time based on the tracked position of the target. Each of the sub-plans is preferably formulated to minimize interplay effects between target movements and MLC leaf movements, consistent with other planning goals. In addition, the sub-plans preferably include a predicted region corresponding to the next anticipated position of the target, in order to facilitate the transition to the next position.
