Endoscope is used to remove the polyp in themedical diagnosis. Absolute size of polyp has been usually estimated by medical doctor with their empirical judgement using endoscope. However this estimation depends on the experience and skill of medical doctor and it is sometimes necessary to use the medical thread with known size for estimating the size of polyp. This paper aims to help medical doctor by proposing a new approach to estimate the size and 3D shape of polyp as a medical supporting system. This proposed approach uses blood vessel as a target with a known size to estimate the absolute size of polyp. Using sequential two images make it possible to estimate the movement of endoscope and reflectance parameter. The idea of using blood vessel is the key idea of this paper, where color information, labeling, morphology processing are used estimate the size and 3D shape of polyp as a final goal. Experiments with endoscope images are demonstrated to evaluate the validity of proposed approach.