The software for comparative genomic hybridization (CGH) has been developed which runs under the Windows 3.1 or Windows 95 operating system. The software is linked with a commercially available wide use software OPTIMAS for image analysis. The fluorescence intensity measured of FITC and TRITC, and FITC/TRITC ratio along each chromosome are described on the respective ideogram using software EXCEL which is widely distributed as a statistical program. This CGH software was tasted using human malignant tumors, and it was proved to be practically useful.