An endoscope system (10, 100) comprising: a lighting section for applying at least first illumination light and second illumination light, in respective frames, to a region of interest, a wavelength range of the first illumination light being different from a wavelength range of the second illumination light, the region of interest including a blood vessel; an image signal acquisition section (12, 101) having a color image sensor with an array of pixels (60b, 60g, 60r) of at least three primary colors, the image signal acquisition section being configured to image the region of interest in each frame, to image the region of interest illuminated with the first illumination light to acquire three color signals of a first frame, and to image the region of interest illuminated with the second illumination light to acquire three color signals of a second frame; a shift amount calculator for calculating a shift amount between an image of the first frame and an image of the second frame based on the color signals of same color; a registration section for aligning images of predetermined color signals, used for calculating an oxygen saturation level of hemoglobin in blood, out of the color signals of the first and second frames based on the shift amount; an oxygen saturation image generator for producing an oxygen saturation image of the oxygen saturation level based on the predetermined color signals aligned; and a display section for displaying the oxygen saturation image, wherein the three color signals are a blue signal, a green signal and a red signal, and each of the first and second illumination light is white light, and the shift amount calculator is configured to calculate the shift amount between the green images produced based on the green signals. a lighting section for applying at least first illumination light and second illumination light, in respective frames, to a region of interest, a wavelength range of the first illumination light being different from a wavelength range of the second illumination light, the region of interest including a blood vessel; an image signal acquisition section (12, 101) having a color image sensor with an array of pixels (60b, 60g, 60r) of at least three primary colors, the image signal acquisition section being configured to image the region of interest in each frame, to image the region of interest illuminated with the first illumination light to acquire three color signals of a first frame, and to image the region of interest illuminated with the second illumination light to acquire three color signals of a second frame; a shift amount calculator for calculating a shift amount between an image of the first frame and an image of the second frame based on the color signals of same color; a registration section for aligning images of predetermined color signals, used for calculating an oxygen saturation level of hemoglobin in blood, out of the color signals of the first and second frames based on the shift amount; an oxygen saturation image generator for producing an oxygen saturation image of the oxygen saturation level based on the predetermined color signals aligned; and a display section for displaying the oxygen saturation image, wherein the three color signals are a blue signal, a green signal and a red signal, and each of the first and second illumination light is white light, and the shift amount calculator is configured to calculate the shift amount between the green images produced based on the green signals.