Structural chromosomal rearrangements can lead to a wide variety of serious clinical manifestations, including mental retardation (MR) and congenital malformations. Over the last years, rearrangements below the detection level of conventional karyotyping have proven to contribute significantly to the cause of MR. These so-called copy number variations are now routinely being detected using various high-resolution microarray platforms targeting the entire human genome. In addition to their clinical diagnostic use, the introduction of these high-resolution platforms has facilitated identification of novel microdeletion and microduplication syndromes as well as disease genes. The aims of this review are to address several aspects of this revolutionizing technology including its application in the diagnostics of MR, the identification of novel microdeletion and microduplication syndromes and the finding of causative genes for known syndromes. In addition, we provide a future prospect for the detection of disease-causing mutations and structural variants by next generation sequencing technologies.