After the fundamental discovery in 1956 that normal human cells contain 46 chromosomes, clinical cytogenetics was born and studies into the relation of chromosomal defects and disease could begin. Although many technical advances have been made over this long period, including the introduction of molecular techniques, until now, all cytogenetic studies have been performed through regular microscopes, which was throughout the years the most important equipment of a cytogenetic laboratory. However, recently a new technique has been introduced based on comparative genomic hybridization on an array of thousands of different probes (array-CGH). This technique enables an increase in the sensitivity of detecting chromosomal aberrations far beyond the detection limit of regular banding techniques. Furthermore, it gives us the possibility to detect genomic changes in malignant cells in cases where aberrations are too complex to study or when chromosomes are not available at all. Cytogenetic laboratories are now challenged to introduce and incorporate this new application next to the various well-established microscopical techniques to provide optimal diagnostic services.