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Gastroenterologists using wireless capsule endoscopy (WCE) extract valuable information regarding the health condition of the intestine. WCE produces, however, near 50,000 frames that have to be examined. In this paper a registration methodology is presented to reduce the amount of frames, which are the same or similar. It utilizes a segmentation scheme and a graph method to register similar regions in two consecutive frames. In addition our methodology offers a degree of similarity between two frames using a confidence function of similarity, in order to discard extremely dissimilar frames and thus set a mark of a new series of frames. Finally, a useful feature called Center of Image Similarity is also presented. Illustrative results from the methodology are also given in this paper.