1. An alignment apparatus comprising: radiation image storage means for storing two radiation images obtained by irradiating radiations on a predetermined body part including two or more tissues; evaluation means for calculating an evaluation value that evaluates an amount of positional shift of the radiographed tissues between the two radiation images, in each of portions of the two radiation images; search condition setting means for setting for each of the portions of the two radiation images a condition of search for corresponding positions between the two radiation images, according to the evaluation value obtained by the evaluation means regarding a corresponding one of the portions of the two radiation images; and alignment means for aligning the two radiation images by searching for the corresponding positions according to the search condition having been set and by warping at least one of the two radiation images.