Using a combined sample (N = 1,215) of referred children and children from the general population aged between 8 and 14 years, the present study addressed two research goals: First, latent mean differences (depending on the individual's sex or psychopathology level) in anxiety, depression, Positive Affect (PA), Negative Affect (NA) and Physiological Hyperarousal (PH) were examined. Secondly, the structure of anxiety and depression was investigated from a tripartite model perspective in boys and girls with high versus low levels of psychopathology respectively. When relating the latent mean level differences in NA, PA, and PH with those in anxiety and depression, the results suggest that higher levels (depending on the individual's sex and psychopathology status) of anxiety or depression are associated with higher levels of PH and lower levels of PA, whereas no consistent pattern was found between mean level differences in NA on the one hand and mean level differences in anxiety/depression on the other. Results further demonstrated that a better fit was obtained for the dual than for the unitary construct representation in boys or girls with high or low levels of psychopathology, thereby suggesting that a valid distinction can be made between anxiety and depression in children between 8 and 14 years old, irrespective of their sex or level of psychopathology. However, when looking at the structural relations of the dual construct representation of anxiety and depression with NA, PA and PH in each of the four groups separately, it became evident that the PH and PA tripartite dimensions could not account for the unique aspects of anxiety and depression respectively. Moreover, PH rather than NA was found to be common for anxiety and depression.