The image pickup system for performing noise reduction processing on signals from an image pickup element comprises a first noise estimating unit for estimating a first amount of noise on the basis of a target pixel in the signals for which noise reduction processing is performed, an extraction unit for extracting similar pixels that resemble the target pixel from the neighborhood of the target pixel on the basis of the target pixel and the first amount of noise, a second noise estimating unit for estimating a second amount of noise from the target pixel and the similar pixels, and a noise reduction unit for reducing the noise of the target pixel on the basis of the second amount of noise.