The present invention aims to provide a gene expression image constructing method and a gene expression image constructing system being able to three-dimensionally show expression patterns of a vastly larger number of genes (specifically, about 30,000 genes). In the present invention, a sample is cut, images of sections of the cut sample are picked up and a stereoscopic image of sample, which is a three-dimensional image of the sample, is constructed based on a plurality of picked-up section images, the amount of expression of genes present in the sample is measured based on a plurality of slices prepared when the sample is cut, and a gene expression image in which an expression state of genes present in the sample and a stereoscopic image of sample are associated with each other is constructed based on a predetermined image reconstruction technique from the constructed stereoscopic image of sample and the measured amount of expression.