There is provided an image pickup system including: a light source apparatus (3) supplying illuminating light an image forming optical system (11) forming an optical image of a subject varying a focus position an image pickup section (12) picking up the optical image and outputting the image a brightness detecting section (23) detecting brightness of the image an auxiliary AF section (27) estimating a temporary focus position based on the brightness of the image detected by the brightness detecting section (23) a control section (24) setting a range which includes the temporary focus position and which is smaller than a whole scanning range as a scanning range and a contrast AF section (26) performing contrast AF within the scanning range.
