Abstract: Intestinal motility analysis is an important examination in detection of various intestinal malfunctions. One of the big challenges of automatic motility analysis is how to compare sequence of images and extract dynamic paterns taking into account the high deformability of the intestine wall as well as the capsule motion. From clinical point of view the ability to align endoluminal scene sequences will help to find regions of similar intestinal activity and in this way will provide a valuable information on intestinal motility problems. This work, for first time, addresses the problem of aligning endoluminal sequences taking into account motion and structure of the intestine. To describe motility in the sequence, we propose different descriptors based on the Sift Flow algorithm, namely: (1) Histograms of Sift Flow Directions to describe the flow course, (2) Sift Descriptors to represent image intestine structure and (3) Sift Flow Magnitude to quantify intestine deformation. We show that the merge of all three descriptors provides robust information on sequence description in terms of motility. Moreover, we develop a novel methodology to rank the intestinal sequences based on the expert feedback about relevance of the results. The experimental results show that the selected descriptors are useful in the alignment and similarity description and the proposed method allows the analysis of the WCE.