A system and method identifies Post Traumatic Stress Disorder by the use of magnetic resonance spectroscopy (MRS) to measure absolute and relative concentrations of metabolites in specific brain regions in the central nervous system or brain. The system and method can be used as a diagnostic tool for the assessment of PTSD. These chemical changes in the brain of those people suffering from PTSD are different from those suffering from head injury, chronic pain and other neurological conditions.