Microarray-based comparative genomic hybridization (array CGH) has revolutionized clinical cytogenetics, as it provides a relatively quick method to scan the genome for gains and losses of chromosomal material with significantly higher resolution and greater clinical yield than was previously possible. A number of different array CGH platforms have emerged and are being used successfully in the diagnostic setting. In the past few years, these new methodologies have led to the identification of novel genomic disorders in patients with developmental delay/mental retardation and/or multiple congenital anomalies (DD/MR/MCA) as well as the discovery that each individual carries inherited copy number variations (CNV) whose contributions to genetic variation and complex disease are not yet well understood. Although array CGH is currently being used as an adjunct test to standard karyotype analysis, it is likely to become the genetic test of choice, especially in cases of idiopathic MR/MCA.