In order to explore the mechanisms of illness course and outcome and to improve treatment in schizophrenia and affective disorders, a theoretical framework as provided by the biopsychosocial concept, e. g. the vulnerability-stress-coping model, has been applied. To develop a coherent and valid research strategy, however, respective model components have to be translated into neuroscience concepts and operationalized accordingly. Course characteristics (typologies, markers), course influences (determinants, triggers, modifiers) and course predictors are discussed from a theoretical perspective. Building on this discussion, an integrative concept of illness course and course mechanisms is proposed. Finally, further research recommendations are given. Future research should elaborate on the neurobiological characteristics of course and outcome in methodologically adequate prospective interventional long-term studies.