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Genetic testing is available and widely used in the neonatal intensive care setting for a broad range of complex presentations arising both antenatally and in the postnatal period. Here we discuss the investigations currently available to clinicians in the neonatal intensive care unit, such as array comparative genomic hybridization (aCGH), FISH (fluorescent in situ hybridization) and quantitative florescent polymerase chain reaction (QF-PCR), later looking to the future of clinical genomic testing, in the form of next generation sequencing panels (NGS panels), whole exome (WE) and whole genome (WG) sequencing. The mainstreaming of genetic medicine requires non-genetic specialists, such as neonatologists and paediatricians, to have confidence and knowledge of the testing process, the technologies available and the ethical and social considerations associated with their use.