An image pickup system includes an image pickup apparatus in which, photoelectric conversion cells are arranged two-dimensionally, and at least some of the photoelectric conversion cells are arranged to output a signal for detecting an amount of defocus. The photoelectric conversion cells which output the signal for detecting the amount defocus form at least two photoelectric conversion cell groups, each receiving a light beam from a pupil area having different area. Each photoelectric conversion cell group has a plurality of photoelectric conversion cell columns. The image pickup system includes a calculating section which has an AF mode which generates a defocus signal by comparing mutually the signals for detecting the amount of defocus which have been output from the two photoelectric conversion cell groups, and a correction section which corrects the signal for detecting the amount of defocus, from information related to distortion of the taking lens.