An endoscope system includes: an image storage section that stores three-dimensional image information in a subject acquired in advance a virtual endoscopic image generating section that generates a virtual endoscopic image endoscopically depicted from a predetermined view point position on the three-dimensional image information an image pickup section that is provided in an endoscope and picks up an image in the specified luminal organ a position detection section that detects a position of a distal end of an endoscope insertion portion in the specified luminal organ and a candidate information presentation section that presents candidate position information to be a candidate when performing image comparison between the virtual endoscopic image and the endoscopic image generated by image pickup by the image pickup section, and the corresponding virtual endoscopic image, as candidate information, on a two-dimensional tomographic image which is obtained by cutting the three-dimensional image information in a predetermined direction based on the position information of the distal end of the endoscope insertion portion by the position detection section.
