Background Little is known regarding changes in the hypothalamic‐pituitary‐adrenal axis (HPA axis) of adolescent girls with and without posttraumatic stress disorder (PTSD) who have recently experienced sexual abuse. Therefore, in this pilot study, we utilized non‐stressed home saliva collection three times a day for three days to assess the levels, diurnal variation and awakening response of cortisol in recently sexually abused adolescent girls. Methods Twenty‐four adolescent girls (mean age: 15 ± 1.5 years) with a history of recent sexual abuse (sexual abuse occurred 1–6 months prior to study enrollment) and 12 healthy, nontraumatized comparison subjects (mean age: 14.8 ± 1.3 years) collected saliva at home upon awakening, 30 min after waking, and in the late afternoon on three consecutive school days. Results Among sexually abused girls, flattening of the morning cortisol awakening response was associated with PTSD severity (r = −.41, P < .05) as well as intrusive symptoms (r = −.42, P < .05). Increased adversity prior to sexual abuse was also associated with flattening of the cortisol awakening response (r = −.53, P < .01). Conclusions Attenuation of the cortisol awakening response in recently sexually abused girls suggests that alterations in HPA‐axis functioning may occur relatively proximate to the traumatic event and correlate with symptom severity of PTSD, intrusive symptoms, and hyperarousal symptoms. These data raise the possibility that subacute alterations in the dynamic secretion of cortisol are directly related to the pathophysiology of sexual abuse‐related PTSD symptoms in adolescent girls.