The United States Food and Drug Administration (FDA) recently signaled its interest in subjecting clinical investigations that employ high-throughput gene sequencing, also called next-generation sequencing, to the agency's Part 812 investigational device exemption (IDE) regulation. Genome sequencing--for reasons explained in this article--blurs the line between categories of in vitro diagnostic (IVD) research that FDA traditionally has regulated and categories of research that FDA traditionally has not regulated. This blurring creates a risk that FDA may overstep its proper authority to regulate fundamental genomic and medical research. This article surveys the legal limits of FDA's authority'to subject genomic research to its IDE requirements. Section 1 explains that FDA has authority to regulate clinical investigations of devices, but is not authorized to regulate investigations that merely use devices to expand medical knowledge or to conduct fundamental research, unless special circumstances apply. Section 2 discusses the special circumstances that can expand or limit FDA's authority to regulate a specific clinical investigation, and Section 3 demonstrates these using an example. Section 4 explores concerns that arose in recent years about risks to human subjects in a certain type of investigation known as sponsor-investigator studies. In response to these concerns, FDA has suggested that it can regulate such studies in ways that threaten to expand FDA's regulation of research at academic medical centers beyond its proper scope. These concerns, while valid in some academic research contexts, seem inapposite in the setting of genomic research programs funded by responsible.entities such as the National Institutes of Health (NIH). Moreover, FDA's regulations do not. appear to support the proposition that FDA can regulate sponsor-investigator studies more expansively than it regulates other studies. Section 5 explores specific ways that NIH, clinical investigators, and FDA might work together to rationalize FDA's regulation of NIH-funded-genomic research.