An endoscope system, comprising: an image acquisition unit that acquires an image obtained by imaging an observation target with an endoscope; an extraction unit that extracts a structure included in the observation target from the image; an index value calculation unit that calculates a plurality of index values based on the structure extracted by the extraction unit; a determination unit that determines whether each of the plurality of index values is a normal value indicating a normal state or an abnormal value different from the normal value; a color information setting unit (78, 100) that sets color information for an abnormal index value, which is the index value determined to be the abnormal value by the determination unit, or sets color information for a normal index value, which is the index value determined to be the normal value by the determination unit; and an image generation unit that generates an emphasized image, in which the structure is emphasized, based on the color information set by the color information setting unit, wherein the color information is a plurality of pieces of information, and a priority is set for each of the pieces of color information, there is a plurality of the abnormal index values or a plurality of the normal index values, and a priority is set for each of the plurality of abnormal index values or the plurality of normal index values, the color information setting unit assigns the color information having a higher priority to the abnormal index value or the normal index value having a higher priority among the abnormal index values or the normal index values, characterized by a priority changing unit that changes the priority set for each of the abnormal index values or the normal index values based on observation conditions, wherein the color information setting unit performs the assignment according to the changed priority, and an endoscope identification unit that identifies whether the endoscope is an upper observation endoscope used for observing the upper digestive tract or a lower observation endoscope used for observing the lower digestive tract, wherein in a case where replacement between the upper observation endoscope and the lower observation endoscope is performed as the observation conditions, the priority changing unit changes the priority of each of the abnormal index values or the normal index values. an image acquisition unit that acquires an image obtained by imaging an observation target with an endoscope; an extraction unit that extracts a structure included in the observation target from the image; an index value calculation unit that calculates a plurality of index values based on the structure extracted by the extraction unit; a determination unit that determines whether each of the plurality of index values is a normal value indicating a normal state or an abnormal value different from the normal value; a color information setting unit (78, 100) that sets color information for an abnormal index value, which is the index value determined to be the abnormal value by the determination unit, or sets color information for a normal index value, which is the index value determined to be the normal value by the determination unit; and an image generation unit that generates an emphasized image, in which the structure is emphasized, based on the color information set by the color information setting unit, wherein the color information is a plurality of pieces of information, and a priority is set for each of the pieces of color information, there is a plurality of the abnormal index values or a plurality of the normal index values, and a priority is set for each of the plurality of abnormal index values or the plurality of normal index values, the color information setting unit assigns the color information having a higher priority to the abnormal index value or the normal index value having a higher priority among the abnormal index values or the normal index values, characterized by a priority changing unit that changes the priority set for each of the abnormal index values or the normal index values based on observation conditions, wherein the color information setting unit performs the assignment according to the changed priority, and an endoscope identification unit that identifies whether the endoscope is an upper observation endoscope used for observing the upper digestive tract or a lower observation endoscope used for observing the lower digestive tract, wherein in a case where replacement between the upper observation endoscope and the lower observation endoscope is performed as the observation conditions, the priority changing unit changes the priority of each of the abnormal index values or the normal index values. a priority changing unit that changes the priority set for each of the abnormal index values or the normal index values based on observation conditions, wherein the color information setting unit performs the assignment according to the changed priority, and an endoscope identification unit that identifies whether the endoscope is an upper observation endoscope used for observing the upper digestive tract or a lower observation endoscope used for observing the lower digestive tract, wherein in a case where replacement between the upper observation endoscope and the lower observation endoscope is performed as the observation conditions, the priority changing unit changes the priority of each of the abnormal index values or the normal index values.