To provide an analysis method and device which is capable of appropriately performing alignment processing in analysis of a DNA chip where a positive control is not arranged as well as in analysis of a chip where a sample includes a small DNA amount.

In the microarray analysis method, a microarray where probes are arranged on a substrate surface having a rugged shape is irradiated with excitation light and fluorescence amounts from respective probes excited by the excitation light are obtained as numeric data. The microarray analysis method includes a step (a) of measuring fluorescence amounts of the probes to acquire fluorescent image data, a step (b) of receiving self-fluorescence from the substrate surface and acquiring the rugged shape of the substrate surface of the microarray from the intensity of received fluorescence as image data for alignment, and a step (c) of determining positions of respective probes in the fluorescent image data on the basis of the image data for alignment.