An endoscope system includes an image pickup section, an insertion section, a first optical system configured to project a first subject image onto the image pickup section, a second optical system configured to project a second subject image onto the image pickup section, an image generating section configured to generate an image based on the first subject image and the second subject image, an image processing section configured to perform predetermined image processing, and a storing section configured to record image processing target region information, and the image processing section moves an image processing region from a region set in the image processing target region information and sets the image processing region so as to coincide with a boundary region between the first subject image and the second subject image.
