In the past three decades, there has been an explosion in research to understand the mechanisms of brain function. Recent advances in psychophysiology and neuroscience, while still limited, have sparked great interest in developing technologies that could peer into the brain and be used to identify or indicate certain behaviors. The polygraph (lie detector) represents an old technology used for discerning clues to the human brain; functional magnetic resonance imaging (fMRI) represents one of the newest efforts. The use of these technologies in intelligence and counterintelligence in the field without validation represents a major concern about its usefulness. Both research on this new technology and subsequent use on public raise ethical challenges. This article will address the overall ethical issues associated with these new technologies. The report identifies the ethical and cultural challenges in conducting research on these new tools, explores the possibility of using current U.S. regulatory requirements regarding drugs and devices as a model for regulating these new technologies, and suggests approaches for the future.