A method and system of compensation for intra-operative organ shift of a living subject usable in image guide surgery. In one embodiment, the method includes the steps of generating a first geometric surface of the organ of the living subject from intra-operatively acquired images of the organ of the living subject, constructing an atlas of organ deformations of the living subject from pre-operatively acquired organ images from the pre-operatively acquired organ images, generating a second geometric surface of the organ from the atlas of organ deformations, aligning the second geometric surface of the organ to the first geometric surface of the organ of the living subject to determine at least one difference between a point of the first geometric surface and a corresponding point of the second geometric surface of the organ of the living subject, which is related to organ shift, and compensating for the intra-operative organ shift.