In recent decades, there has been a steady increase in the number of people, including adolescents, undergoing medical body modification (MBM) to alter their physically healthy bodies in invasive and nearly irreversible ways through medical treatment (e.g. surgery). While MBM is often recommended for youth with persisting gender dysphoria (GD), in body dysmorphic disorder (BDD) it has been considered contraindicated. Here, we outline the current controversies surrounding MBM practice and recommendations in adolescents with GD versus those with BDD in order to better understand under what circumstances we may or may not support adolescents who want to change their bodies medically and often irreversibly. We compare the two disorders in terms of the overlap and uniqueness of their behavioural and psychological features. In doing so, we discuss limitations of the existing (often low-quality) evidence for and against MBM in young patients. We conclude that the currently available evidence is too preliminary and far from conclusive to make any robust recommendations in terms of benefits and harms of MBM in youth with persisting GD or BDD. However, we strongly recommend further urgent scientific discussions and systematic research efforts into more robust evaluations and the identification of more precise psychological characteristics that may serve as decision criteria for or against MBM – particularly in those adolescents who did not respond to non-MBM, that is, psychiatric/psychological treatment and psychosocial support, if available at all. This will greatly benefit youth healthcare professionals in their challenging clinical practice of making decisions regarding MBM today and in the future.