This chapter explores how integrating artificial intelligence into clinical settings impacts the autonomy of physicians and patients. Focusing on advanced systems such as large language models and clinical decision support systems, this chapter examines the dual impact of AI on clinical decision-making. For physicians, computational and value opacity, regulatory ambiguity, automation bias, and deskilling can compromise professional independence. Simultaneously, transitive paternalism and relational opacity, which hinder truly informed consent and participatory decision-making, challenge patient autonomy. Nevertheless, artificial intelligence also offers opportunities to enhance autonomy: for physicians, through administrative relief as well as diagnostic assistance, for patients, via wearables, chatbots, and AI surrogates that promote personalized care and independent health management. This chapter emphasizes that safeguarding autonomy in AI-driven medicine requires more than transparency; it demands shared ethical responsibility among developers, institutions, and clinicians. Autonomy must be understood beyond informed consent, focusing on explicability, meaningful engagement, and alignment with patient values and well-being. Ultimately, AI should serve patient well-being.