The adolescent brain undergoes significant structural and functional development. Through the use of magnetic resonance imaging in adolescents, it has been demonstrated that the prefrontal cortex, pertinent for executive control, demonstrates protracted development compared to limbic structures, active during emotion and reward processing. This asynchronous development creates a sensitive window during adolescence, in which many psychopathological disorders (i.e. mental health and substance use) emerge. This review outlines longitudinal studies that use magnetic resonance imaging to identify neurobiological predictors of emergent psychopathology (depression, anxiety and substance use), during adolescence. Studies identifying neurobiological markers that predict onset and escalation of these disorders, as well as those that predict successful treatment outcomes are explored. An emphasis is placed on frontolimbic brain structures, a convergent neurobiological target for both emergent mental health issues and emergent substance use. This knowledge is crucial, as it may be used to develop neurobiologically targeted prevention and intervention strategies for youth who are at-risk for developing these psychopathologies.