An information processing apparatus capable of generating a group of in-vivo images along a route in a digestive canal and a capsule endoscope system are provided. The information processing apparatus includes a storage unit 59 that stores data of the in-vivo images and information which is associated with the data of the in-vivo images and related to a position of the capsule endoscope 2 in an inside of a subject a positional information obtaining unit 54 that obtains positional information of the capsule endoscope 2 in capturing the in-vivo images based on the information related to the position a correlation degree calculator 56 that calculates a degree of correlation between predetermined in-vivo images based on the data of the in-vivo images and a sequence changing unit 55 that changes a sorting sequence of the in-vivo images based on the positional information obtained by the positional information obtaining unit 54 and the degree of correlation calculated by the correlation degree calculator 56.
