Background: Repetitive Negative Thinking (RNT) is assumed to be a transdiagnostic proximal risk factor in depression and anxiety. We examined the prospective relations of disorder-dependent as well as disorder-independent measures of RNT with depression and anxiety outcomes. Methods: In a prospective cohort study, 1972 adults completed a 3-year follow-up period (attrition = 12.6%). DSM-IV diagnoses were assessed with the CIDI, symptom severity with the IDS and BAI, and RNT with measures for perseverative thinking (PTQ), rumination (LEIDS-R) and worry (PWQ). Results: The common dimension of our RNT measurements (according to Confirmatory Factor Analysis) was significantly associated with comorbidity among depressive and among anxiety disorders, severity of depressive and anxiety symptoms, as well as persistence and relapse of depressive and anxiety disorders. Additionally, a specific factor for rumination predicted comorbidity of depressive disorders, comorbidity of anxiety disorders and relapse of depressive disorder, while a specific factor for worry predicted comorbidity of anxiety disorders and relapse of anxiety disorders, although to a lesser extent than general RNT. Limitations: The present study relied solely on self-report measures of RNT and controlling for baseline demographic and clinical variables greatly attenuated the predictive value of RNT. Discussion: Disorder-independent RNT may be a similar underlying process present across depressive and anxiety disorders. It seems more important than the representation of this process in disorder-specific cognitive content such as rumination in depression and worry in anxiety. RNT as a pathological trait deserves more attention in clinical diagnosis and the transdiagnostic treatment of comorbid depression and anxiety in particular.