An efficient, objective, flexible and easily deployable system for conducting evaluations of mental and physiological state and recommending individualized treatment to improve said state is described. The method and system are based on commensurate measurement of mental functions, levels of stress and anxiety, and/or biologically active molecules such as neurotransmitters, immune markers including cytokines and hormones. The method and system are designed to assess an individual's cognitive function and the underlying physiology in order to delineate various disease processes, injuries, drug states, training stages, fatigue levels, stress levels, aging processes, predict susceptibility to stress and/or sleep deprivation, identify aptitude for training and/or characterize effects of any experimental conditions. The system and method may be used in recommending individualized treatment protocols, as well as to guide the treatment process by assessing the efficacy of such therapies in the clinical trials process.