In an imaging apparatus, a method of correcting image data, or a storage medium storing a program, a target is imaged in a plurality of imaging regions and image data is output from each of the plurality of imaging regions; based on the image data captured in a first imaging operation, an imbalance in output levels of image data respectively output from the plurality of imaging regions in a second imaging operation is corrected; and an imaging condition in the first imaging operation is controlled in accordance with an imaging condition in the second imaging operation. Accordingly, an imbalance in a plurality of image data simultaneously output from a plurality of output terminals of an imaging device is automatically corrected appropriately even if an imaging condition changes.