Elevated salivary cortisol levels have been documented in individuals who engage in self-injurious behavior (SIB), indicating acute physiological stress. Less is known about the chronicity of stress and SIB. We analyzed the relationship between parent ratings of problem behavior and hair cortisol concentrations (an index of chronic adrenocortical activity) in 23 children with autism spectrum disorder (ASD). Parent ratings of problem behavior were not significantly correlated with hair cortisol concentrations. When children were categorized into groups based on the frequency and severity of SIB, participants with the greatest frequency and severity of SIB had higher hair cortisol concentrations compared to children without SIB. Frequent and severe SIB may be associated with altered hypothalamic-pituitary-adrenal (HPA) axis activity in children with ASD.