A focus detection apparatus which is capable of estimating each of signals from a plurality of split PDs, which are included in a sum signal from split PDs, by performing a computation to thus detect saturation with respect to each split PD. With respect to each unit pixel cell having a plurality of PDs sharing one micro lens, saturation of a pixel signal read out in a non-destructive manner from one of the PDs is detected. Based on a first luminance signal and a sum pixel signal obtained by summing signals output from the PDs, another pixel signal output from another one of the PDs is estimated. Saturation of the estimated pixel signal is detected, and a second luminance signal is generated. Based on the first and second luminance signals, the amount of defocus for an optical unit is calculated.