Recent advances in the clinical application of genomic technologies have significantly impacted the field of prenatal diagnosis. Central to these advances has been the implementation of chromosomal microarray analysis (CMA). Microdeletions and microduplications, undetectable by traditional karyotyping, have recently been confirmed to play a role in altered neurocognitive development. CMA is now recommended for fetuses with structural anomalies. However, CMA comes with an increased need and role for genetic counseling, because the potential genomic information available is exponentially increased. CMA also can be performed on a small number of preimplantation embryonic cells for assessment of the embryo's reproductive potential. Implementation of these new genomic techniques in an in vitro fertilization setting has already demonstrated significant improvements in reproductive outcome. Techniques are now being developed to eliminate the necessity for invasive prenatal diagnosis procedures. Currently in its infancy, noninvasive prenatal testing using cell-free fetal DNA from maternal blood has already improved the sensitivity for detection of the common aneuploidies and current efforts are focused on identifying select microdeletions. The explosion of new genomic technologies continues to offer great benefits. However, each needs critical assessment prior to adoption in a clinical setting.