A medical image processing apparatus and a program are shown. The medical image processing apparatus includes an emphasizing processing unit, a positioning unit, and a difference image generating unit. The emphasizing processing unit performs processing to emphasize a specific structure among structures composing a subject on each of a first image and a second image obtained by capturing the same subject at different points in time. The positioning unit matches a position of the specific structure in the first image and the second image based on the first image and the second image with the specific structure emphasized. The difference image generating unit generates a difference image between the first image and the second image with the position of the specific structure matched.
