The use of ultrahigh throughput diagnostic tests that determine genetic sequence variation to guide patient care is rapidly expanding, fueled by the enormous growth in sequencing platform development. With the emergence of novel technologies, the FDA is faced with new regulatory challenges while continuing to apply scientific evidence-based oversight. While there are no broadly accepted standards or methods to analytically validate ultrahigh throughput sequencing tests yet, there are a number of efforts underway, including establishing reference materials to aid in assessing analytical performance. The additional challenge in informed clinical application of sequence information is inadequate knowledge about correlations between genomic variations and their clinical significance. The FDA is proactively working to encourage cross-collaboration in this area. Ultimately, the FDA has to balance public safety concerns with fostering innovation and enabling the translation of emerging technologies that can improve medical care and benefit public health.