Background: Literacy difficulties show high levels of comorbidity with both disruptive and emotional disorders, but questions remain over the nature and specificity of these links. Method: Relationships between specific literacy difficulties and psychiatric disorder were investigated in a large-scale national sample of children aged 9 to 15 years. Results: Specific literacy difficulties were more common in children from lower socio-economic backgrounds, and were significantly associated with increased risks of Attention-Deficit Hyperactivity Disorder (especially inattentive symptomatology), Conduct Disorder and anxiety disorders in both girls and boys, and with self-reports of depressed mood in boys. Associations between literacy difficulties and diagnoses of both Attention-Deficit Hyperactivity Disorder (ADHD) and Conduct Disorder (CD) were mediated by inattentiveness, as were links with low mood. Links between specific literacy difficulties and anxiety were of a different nature, suggestive of a direct impact of literacy problems on risk for anxiety disorders. Conclusions: Literacy difficulties are significantly associated with externalising disorders via inattention, but may constitute a more immediate risk factor for naturally anxious children to develop clinically significant levels of anxiety. (Contains 1 figure and 3 tables.)