Most scholars believe assisted reproductive technology is subject only to minimal regulation, especially by the federal government. This belief, I contend, is wrong. In this Article, I examine agency documents, statements by officials, and letters that the U.S. Food and Drug Administration (FDA) has sent to physicians and researchers over the past fifteen years to reveal an overlooked regulatory program. The FDA has been targeting new forms of assisted reproductive technology that involve small genetic modifications (advanced assisted reproductive technologies or AARTs) through regulatory actions that receive little public, media, or scholarly attention. I term this method of regulation “subterranean regulation.” Subterranean regulatory actions chill research as many physicians and researchers halt their research after receiving these letters or stop providing access to AARTs in the United States.