This narrative review explores the potential, complexities, and consequences of using artificial intelligence (AI) to screen large government-held facial image databases for the early detection of rare genetic diseases. Government-held facial image databases, combined with the power of artificial intelligence, offer the potential to revolutionize the early diagnosis of rare genetic diseases. AI-powered phenotyping, as exemplified by the Face2Gene app, enables highly accurate genetic assessments from simple photographs. This and similar breakthrough technologies raise significant privacy and ethical concerns about potential government overreach augmented with the power of AI. This paper explores the concept, methods, and legal complexities of AI-based phenotyping within the EU. It highlights the transformative potential of such tools for public health while emphasizing the critical need to balance innovation with the protection of individual privacy and ethical boundaries. This comprehensive overview underscores the urgent need to develop robust safeguards around individual rights while responsibly utilizing AI’s potential for improved healthcare outcomes, including within a forensic context. Furthermore, the intersection of AI and sensitive genetic data necessitates proactive cybersecurity measures. Current and future developments must focus on securing AI models against attacks, ensuring data integrity, and safeguarding the privacy of individuals within this technological landscape.