Because genetic conditions can alter the health of neonates, it is important for neonatologists to become familiar with the indications for testing and major issues in the interpretation of results. The two primary molecular cytogenetic techniques are fluorescence in situ hybridization and array comparative genomic hybridization, which allow detection of deletions, duplications, and rearrangements of small regions within the chromosome. Direct mutation analysis of DNA can be targeted to a specific variant known to be associated with disease. Epigenetic factors can affect gene expression without altering the genotype. For example, genomic imprinting (differential expression of a gene) causes several genetic disorders. Most molecular genetic testing performed in the newborn nursery is for purposes of diagnosis. Important differences in analytic validity, clinical validity, and clinical utility distinguish genetic testing from more traditional laboratory testing, and the implications of these differences must be considered when ordering such tests.