Until recently, the prenatal detection of genetic disease was available to only a subset of the pregnant population deemed to be at an increased risk for chromosomal abnormalities or, more rarely, other genetic disorders, based on family history, multiple-marker screening or ultrasound findings. Guided by recent data that indicate that screening for Down syndrome has improved and that risks of invasive procedures are smaller than previously ascertained, the American College of Obstetricians and Gynecologists has recommended that all women have access to invasive prenatal diagnosis. The parallel development of newer genetic diagnostic technologies, such as chromosomal microarray analysis, has made it feasible to simultaneously test for more conditions than was possible with standard karyotype analysis complemented by targeted fluorescence in situ hybridization or mutation detection for specific conditions. In the pediatric and adult population, chromosomal microarray analysis has already been thoroughly evaluated and is now recommended as a first-line diagnostic test for clinically suspected genetic disorders. In this article, we review the current status of array-based comparative genomic hybridization use for prenatal diagnosis and predict that, in the future, it will replace karyotyping as a first-line test for detecting chromosomal abnormalities in the prenatal setting.