Chromosomal rearrangements are an important cause of distinctive and recognizable clinical phenotypes. For many years conventional karyotyping has been a successful tool to detect such chromosomal rearrangements. However, this technique has a limited resolution of 5–10 Mb. In the past decades, the development of new high-resolution techniques has led to the field of molecular cytogenetics. One of the most significant changes has been the use of molecular karyotyping by high-resolution whole-genome array techniques in the diagnostic setting. This technology is able to detect chromosomal aberrations at a resolution beyond the detection level of conventional karyotyping. Many new microdeletion and microduplication syndromes have been identified by this new method. In this review, we will focus on the most commonly used (molecular) cytogenetic techniques.