This study inquires into neurobiological response to stress and its clinical correlates among adolescents with post-traumatic stress disorder (PTSD). Structural magnetic resonance imaging (MRI) measures of cerebral anatomy were carried out on 23 female adolescents with PTSD related to severe childhood sexual abuse and 21 matched healthy controls. Clinician Administered PTSD Scale for Children and Adolescents, Adolescent Dissociative Experiences Scale, Childhood Trauma Questionnaire, Schedule for Affective Disorders and Schizophrenia for School Age Children, Beck Depression Scale, and a set of neuro-cognitive tests were administered to all participants. Compared to controls, PTSD group bilaterally had smaller amygdala, hippocampus, anterior cingulate, and thinner prefrontal cortex but normal thalamus. Further analyses within the PTSD group suggested an association between symptoms of PTSD and sizes of right brain structures including smaller amygdala but larger hippocampus and anterior cingulate. Thinner right prefrontal cortex and larger right thalamus seemed to be related to denial and response prevention, respectively. Being related to both hemispheres, dissociative amnesia was negatively associated with proportion of the right amygdala to right thalamus and to both left and right prefrontal cortex. Suggesting a neuro-protective effect against traumatic stress at least through adolescence, depersonalization-derealization and identity alteration were correlated with thicker left prefrontal cortex. Unlike the lateralization within PTSD group, correlations between regions of interest were rather symmetrical in controls. The graded response to stress seemed to be aimed at mental protection by lateralization of brain functions and possibly diminished connection between two hemispheres. A Tri-Modal Reaction (T-MR) Model of protection is proposed.