Elevated cortisol and cognitive impairments have been described in anorexia nervosa, but the relationship between these two variables has not been adequately explored. We profiled the pattern and extent of the cognitive impairment in anorexia nervosa and determined how this related to cortisol secretion. Twenty patients with anorexia nervosa and a matched control group completed a computerized cognitive assessment battery. Diurnal cortisol secretion was measured by serial saliva sampling. Patients were significantly impaired on tasks of attention, long-term memory and working memory. Both groups showed the expected diurnal variation in cortisol production, but no evidence was found for patient cortisol hypersecretion. No correlation was found between cortisol secretion and any of the cognitive task measures. These data suggest that at least some of the cognitive impairments seen in anorexia nervosa are attributable to something other than a basal increase in cortisol secretion. The limitations of cortisol as an indicator of HPA axis activity are discussed.