There is provided an image registration device, method, and program capable of performing registration between two images obtained by imaging a subject configured to include parts of a plurality of bones, such as the vertebral column, with high accuracy. The image registration device includes: a medical image acquisition unit that acquires first and second three-dimensional images by imaging a subject configured to include parts of a plurality of bones at different points in time an identification unit that identifies the parts of the plurality of bones included in each of the first and second three-dimensional images a matching unit that matches a part of each bone included in the first three-dimensional image with a part of each bone included in the second three-dimensional image and a registration processing unit that performs registration processing between images of the matched parts of the bones.
