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Shared difficulties with cognitive control may play a role in co-occurring mental health problems frequently observed in autistic children. We investigated how different cognitive control processes (inhibitory control, conflict resolution, cognitive flexibility) associated with traits of autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD) and anxiety in 7-year-old children at elevated (n = 44) and typical (n = 37) familial likelihood for ASD. Poor inhibitory control was associated with higher ADHD traits. Better inhibitory control and poorer cognitive flexibility predicted higher anxiety traits. Cognitive control processes were not associated dimensionally with autistic traits, though better conflict resolution predicted greater likelihood of meeting diagnostic criteria for ASD in categorical analysis. These findings suggest that different cognitive control alterations are associated with ASD, ADHD and anxiety.