The widespread use of array comparative genomic hybridization (CGH)for the diagnosis of genomic rearrangements in children with idiopathic mental retardation,developmental delay, and multiple congenital anomalies has spurred interest in applying array CGH technology to prenatal diagnosis. The use of array CGH technology in prenatal diagnosis is currently limited by several factors, including the inability to detect balanced chromosomal rearrangements, the detection of copy number variations of uncertain clinical significance, and significantly higher costs than conventional karyotype analysis. Although array CGH has distinct advantages over classic cytogenetics in certain applications, the technology is not currently a replacement for classic cytogenetics in prenatal diagnosis.