Many mental disorders debut during adolescence, a period also characterised by substantial brain development. The interplay of preceding factors and how they relate to neurodevelopmental trajectories of mental illness is not well understood. Here, we used canonical correlation and independent component analysis to estimate modes of covariation between structural neuroimaging measures with cognitive, clinical, and environmental measures in a clinical youth sample. We then performed out-of-sample validation of the detected brain-patterns in an independent non-clinical sample of youth with a similar age range. The brain patterns were estimated using the Healthy Brain Network cohort, in participants aged 5-21 (n=1732, 64% male), with the majority meeting the criteria for at least one psychiatric disorder. These analyses identified two significant modes of brain-behaviour covariation: the first linked age, physical and cognitive maturation to brain features including lower cortical thickness and gyrification (r=.92, p=.005). The second mode linked lower language skills, lower academic performance, and social communication and psychological difficulties, with lower white matter surface area and gyrification (r=.92, p=.006). Diagnosed youth showed elevated mode 2 scores compared to undiagnosed peers. Out-of-sample validation of these brain patterns was performed in the Philadelphia Neurodevelopmental Cohort in largely undiagnosed youth aged 8-21 (n=1253, 54% female). We replicated the covariation pattern across brain features for both modes. Mode 1 correlated highly with age (r [95% CI]; .7 [.68-.71]) and age-related cognitive maturation (.36 [.33-.38]), while mode 2 correlated with deviations from normative cognitive development (-.24 [-.27 - -.21]). Together, our results identify both expected and novel brain-behaviour patterns, linking maturation and socio-cognitive difficulties to brain structure across diagnostic boundaries. Our results support the notion of aberrant cognitive development as a cross-diagnostic risk factor for mental illness, with a traceable pattern in the youth brain.