In this paper, we first briefly describe neuroimaging technology, our reasons for studying magnetic resonance imaging (MRI) technology, and then provide a discussion of what we have identified as priority issues for paediatric MRI research. We examine the issues of respectful involvement of children in the consent process as well as privacy and confidentiality for this group of MRI research participants. In addition, we explore the implications of unexpected findings for paediatric MRI research participants. Finally, we explore the ethical issues concerning advances in functional MRI. This paper aims to provide a clear description of priority paediatric MRI research ethics issues to make some preliminary recommendations regarding next steps.