Research with adults and older adolescents suggests a general factor may underlie both mental health difficulties and wellbeing. However, the classical bifactor model commonly used to demonstrate this general trait has recently been criticised when a unidimensional structure is not supported. Furthermore, research is lacking in this area with children and early adolescents. We present confirmatory factor analysis models to explore the structure of psychopathology and wellbeing in early adolescents, using secondary data from a large U.K. sample (N = 1982). A simple correlated factors structure fitted the data well and revealed that wellbeing was just as related to internalising as this was to externalising symptoms. The classical bifactor solution also fitted the data well but was rejected as the general factor explained only 55% of the total common variance. S-1 models were therefore used to explore general covariance in a more robust way, and revealed that a general internalising distress factor could play an important role in all item responses. Gender and income differences in mental health were also explored through invariance testing and correlations. Our findings demonstrate the importance of considering mental health difficulties and wellbeing items together, and suggestions are made for how their correspondence could be controlled for.