The relation of symptoms of conduct disorder (CD) and anxiety to salivary cortisol was explored in 67 clinic-referred boys aged 8 to 13 years. Children with anxiety disorder had higher levels of cortisol, but this main effect was qualified by a significant CD x anxiety disorder interaction. Consistent with Gray's biological model of the behavioral inhibition system (BIS), children with both CD and anxiety disorder had higher levels of salivary cortisol than children with CD without comorbid anxiety disorder. In the absence of CD, however, anxiety disorder was not clearly associated with higher cortisol. This result suggests that cortisol may be a useful biological marker of arousal associated with BIS activity in children with CD.