An image pickup system of the present invention has a light emitting section that emits a first illuminating light and a second illuminating light to an object, an image pickup section that picks up an image of a first return light from the object corresponding to the first illuminating light and an image of a second return light from the object corresponding to the second illuminating light, and outputs the images as image pickup signals respectively, an image generating section that generates a first image corresponding to the first return light and a second image corresponding to the second return light respectively based on the image pickup signals, a differential value calculating section that calculates a first differential value corresponding to the first image and a second differential value corresponding to the second image respectively, a calculation section that performs calculation processing by using the first differential value and the second differential value, and a region discriminating section that discriminates between a predetermined region and a region other than the predetermined region in the object by applying threshold processing to a calculation result of the calculation section.
