For depressive and anxiety disorders general course characteristics are known. However, prognosis varies among patients with the same diagnosis. The current study investigated whether the more homogeneous symptom dimensions of mood/cognition and anxiety/arousal, could be used to predict more differentiated prognoses than with overall course-categories. One-thousand-and-fifty-three subjects with a depressive and/or anxiety disorder from the Netherlands Study of Depression and Anxiety (NESDA) were assessed at baseline and at 2-year follow-up. Dimensions of mood/cognition and anxiety/arousal were extracted from the Self Report Inventory of Depressive Symptomatology (IDS-SR). Diagnoses at baseline and follow-up were assessed with a standardized psychiatric interview. Course trajectories were assessed with a life chart interview. Increased mood/cognition scores predicted single depression (OR = 1.80) and comorbid depression-anxiety (OR = 2.00 [CI: 1.28-2.54]) at follow-up and unfavourable course trajectories of depressive symptomatology (OR = 1.94-2.08). Increased anxiety/arousal predicted single panic disorder at follow-up (OR = 2.21 [CI: 1.62-3.03]) and unfavourable course trajectories of anxiety symptomatology (OR = 1.38-1.42). All associations remained significant when adjusted for other prognostic factors, including baseline diagnosis. In conclusion, the widely used IDS-SR can be used to measure two dimensions that contribute prognostic value on top of other, previously known prognostic factors. © 2012 Elsevier Ltd.