Severe antisocial behavior in girls, best exemplified by conduct disorder (CD), is a serious clinical and public health problem. Treatment is difficult, particularly in girls with comorbid internalizing disorders. Identifying biological correlates may help to develop new treatments or diagnostic, prognostic, or treatment response biomarkers. Based on our earlier work and research from others occurring primarily in boys with severe antisocial behavior, it is possible that abnormalities in the hypothalamic pituitary adrenal (HPA) axis circadian cortisol cycle may be associated with female CD. Additionally, research suggests that the presence of comorbid internalizing disorders may be related to differences in cortisol secretion, compared to subjects who only have CD. Our study aimed: 1) to compare the circadian cortisol cycle in 98 girls with CD, 15-16 years of age to 47 girls without any psychiatric disorder (ND) and 2) to compare the cycle in girls with CD and comorbid internalizing disorders (CD + INT) to those without such comorbidity (CD Only). Salivary cortisol was collected over 24 h during weekdays at scheduled times, with protocol adherence measures in place. Unstructured covariance pattern modeling, controlling for effects of age, social class, IQ, and awakening time was used to analyze cortisol data. CD was associated with overall lower cortisol secretion (p = 0.03), but this difference was due to a lower volume of cortisol secreted 30 min after awakening (area under the curve with respect to ground, p = 0.01). Circadian cortisol secretion was no different in the CD+INT group compared to the CD Only group (p = 0.52). Our findings need to be replicated using current consensus guidelines for the assessment of the CAR. We also suggest two new avenues of research in this field.