In recent discussions on the right to freedom of thought (RFoT) it has been emphasised that for an adequate understanding, development, and application of the right, one should consider how the RFoT relates to or complements other rights, such as the right to mental privacy, mental integrity and the freedom of expression. In this chapter, we examine the interrelationship between the RFoT and the protection of mental privacy and mental integrity. Considering the case of employing emerging neurotechnology in criminal justice, we explore how the absolute protection offered by the RFoT relates to the qualified protection of mental privacy and mental integrity offered by the right to respect for private life. We argue that, depending on the interpretation of these rights, they have the potential to overlap, which raises the need to develop a legal mechanism to distinguish absolute from qualified protection of mental privacy and mental integrity. We suggest three general factors that could be relevant in this regard: (1) the mental effects of an interference and the method of inducing them, (2) the victim’s vulnerability, and (3) the context of a mental interference.