Chromosomal aberrations caused by radiation can be well detected using fluorescence in situ hybridization (FISH) technique. Not only numerical and structural changes, but also changes in spatial arrangement of chromosomes can be detected by an appropriate DNA-probe. Using FISH, both metaphase spreads and interphase nuclei can be analysed which is important in case of non-dividing cells. The analysis of FISH-stained microscopic slides can be done either manually or by means of a computer. The second approach is obviously preferable - the analysis is quicker, more precise, not biased and can be automated. Moreover, the compter can work overnight and process large quantities of data. The possibility to analyse a lot of images (i.e. a lot of metaphase spreads or interphase nuclei) is of great value in rare events studies such as radiation-induced aberrations where the percentage of damaged cells is very low for low doses (produced by environmental radiation) and a lot of data is needed for proper statistical scoring. The computer analysis of FISH-stained slides can be divided into three main parts: 1) object searching (finding the metaphase spread or interphase nuclei on the slide), 2) image capture (the image must be captured using a suitable CCD camera, digitized and transfered to the computer memory), 3) image analysis (computer must find the metaphase spreads or interphase nuclei, FISH-signals on them and evaluate the data). This paper describes the advances in automation of these three tasks and, subsequently, the whole process of FISH-stained slides analysis. The paper is concentrated mostly on the system developed in Brno based on Leica DMRXA motorized computer driven microscope, a PC Pentium computer and own software for image acquisition and analysis. The system was already successfully used in several studies including radiation induced changes in human genome.