An endoscope system comprising: a lighting section (31a-31d) for applying measurement light to an internal body part of a subject; an image sensor for imaging the internal body part illuminated with the measurement light to output a color pixel value of each pixel; wherein the image sensor is adapted to image a normal internal body part with no lesion being illuminated with the measurement light in a preliminary imaging, and to image an internal body part with a lesion being illuminated with the meas urement light in a main imaging, a storage section; wherein the storage section is adapted to store standard reference data that defines a correlation between the color pixel value and an oxygen saturation level; and a processor, having a calculation section adapted to calculate a pre-oxygen saturation level of the normal internal body part based on the standard reference data and a pre-color pixel value obtained from the image sensor during preliminary imaging; a changing section adapted to change the standard reference data to corrected reference data in accordance with a difference between the pre-oxygen sat uration level and a predetermined standard value of the oxygen saturation level and the changing section being adapted to store the corrected reference data in the storage section together with the standard reference data; and a control section adapted to execute the preliminary imaging and main imaging, wherein the calculation section is adapted to calculate an oxygen saturation level of the internal body part based on the corrected reference data and a color pixel value obtained from the image sensor during the main imaging. a lighting section (31a-31d) for applying measurement light to an internal body part of a subject; an image sensor for imaging the internal body part illuminated with the measurement light to output a color pixel value of each pixel; wherein the image sensor is adapted to image a normal internal body part with no lesion being illuminated with the measurement light in a preliminary imaging, and to image an internal body part with a lesion being illuminated with the meas urement light in a main imaging, a storage section; wherein the storage section is adapted to store standard reference data that defines a correlation between the color pixel value and an oxygen saturation level; and a processor, having a calculation section adapted to calculate a pre-oxygen saturation level of the normal internal body part based on the standard reference data and a pre-color pixel value obtained from the image sensor during preliminary imaging; a changing section adapted to change the standard reference data to corrected reference data in accordance with a difference between the pre-oxygen sat uration level and a predetermined standard value of the oxygen saturation level and the changing section being adapted to store the corrected reference data in the storage section together with the standard reference data; and a control section adapted to execute the preliminary imaging and main imaging, wherein the calculation section is adapted to calculate an oxygen saturation level of the internal body part based on the corrected reference data and a color pixel value obtained from the image sensor during the main imaging.