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Traditional therapies for posttraumatic stress disorder (PTSD) and the many neuropsychiatric conditions associated with abuse, stress, and combat are effective in only half of patients, despite best efforts and practices. The 50% of patients who do not improve by responding to usual standards of care are labeled treatment resistant. I propose that comorbid medical illnesses and injuries affecting mental state and general health and the failures of the systems that treat them contribute to the so-called “resistance” of chronic PTSD, depression, and anxiety. Military veterans and victims of torture often manifest treatment-resistant PTSD, depression, and anxiety. Many are debilitated by sleep disturbances, anxiety, depression, postconcussion syndrome, hypothyroidism, pain, and degenerative arthritis. Current practices lack an effective model for integrating these medical illnesses and injuries into the diagnosis and treatment of treatment-resistant PTSD, depression, and anxiety. A working model that integrates these components would involve comprehensive and integrated diagnosis and treatment. Current treatment approaches also often fail to track meaningful measures of recovery, most notably quality of life. The application of general systems theory provides a framework to address these deficits by focusing on the complex interplay between the psychological and physiological, recognizing the cumulative and synergistic effects of the psychiatric, neurological, metabolic, and pain problems—both clinical and subclinical—that contribute to treatment-resistant PTSD, depression, and anxiety.