Analysis method and reading device for microarray

In order to provide an analysis method enabling the appropriate performance of alignment processing even in the analysis of a DNA chip where no positive control has been arranged or even in the analysis of a chip where a sample contains little DNA, this microarray analysis method for irradiating, with excitation light, a microarray where probes have been arranged on a substrate surface having an uneven shape, and obtaining as numerical data the amount of fluorescence from each of the probes excited by the excitation light comprises: a step (a) for measuring the amount of fluorescence of the probes and acquiring fluorescence image data; a step (b) for receiving reflected light and/or scattered light from the substrate surface and acquiring, as image data for alignment, the uneven shape of the substrate surface of the microarray, from the intensity of the received light; and a step (c) for determining the positions of each of the probes in the fluorescence image data on the basis of the image data for alignment