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, wherein the two radiation images being obtained by irradiating the radiations having different energy distributions on the body part including the two or more tissues having different radiation absorption characteristics, the alignment apparatus further comprising component image generation means for generating component images regarding at least two of the tissues represented by signal components of the at least two of the tissues by carrying out subtraction processing on the two radiation images, and the evaluation means calculating the evaluation value, by using the signal components at pixels corresponding to each other in the component images generated by the component image generation means.