The current study used confirmatory factor analysis (CFA) to examine the factor structure of anxiety and depressive disorders in a sample of clinic-referred adolescents, aged between 12 and 18 years, for diagnoses based on parent (N = 655; male = 441) and adolescent (N = 626; male = 417) interviews. Three models were examined: a 1-factor model, with all anxiety and depressive disorders in a single factor; a DSM-based 2-factor model, with anxiety disorders in one factor, and depressive disorders in another factor; and an alternate 2-factor model, with fear related anxiety disorders in one factor, and other anxiety and depressive disorders in another factor. The findings indicated support for all three models. Also, ADHD and ODD/CD were associated with only the shared variances between the latent factors in the 2-factor models, and not their unique variance. The implications of the findings for taxonomy, comorbidity, and clinical practice are discussed.