Colonoscopy is an endoscopic technique that allows a physician to inspect the inside of the human colon and to perform--if deemed necessary-at the same time a number of diagnostic and therapeutic operations. In order to see the inside of the colon, a video signal of the internal mucosa of the colon is generated by a tiny video camera at the tip of the endoscope and displayed on a monitor for real-time analysis by the physician. We have captured and stored these videos in digital format and call these colonoscopy videos. Based on new algorithms for instrument detection and shot segmentation, we introduce new spatio-temporal analysis techniques to automatically identify an operation shot--a segment of visual data in a colonoscopy video that corresponds to a diagnostic or therapeutic operation. Our experiments on real colonoscopy videos demonstrate the effectiveness of the proposed approach. The proposed techniques and software are useful for 1) postprocedure review for causes of complications due to diagnostic or therapeutic operations; 2) establishment of an effective content-based retrieval system to facilitate endoscopic research and education; 3) development of a systematic approach to assess and improve the procedural skills of endoscopists.