While much attention has been devoted to examining the beneficial effects of Mindfulness-Based Stress Reduction programs on patients' ability to cope with various chronic medical conditions, most studies have relied on self-report measures of improvement. Given that these measures may not accurately reflect physiological conditions, there is a need for an objective marker of improvement in research evaluating the beneficial effects of stress management programs. Cortisol is the major stress hormone in the human organism and as such is a promising candidate measure in the study of the effects of Mindfulness-Based Stress Reduction programs. In conjunction with other biological measures, the use of cortisol levels as a physiological marker of stress may be useful to validate self-reported benefits attributed to this program. In the current manuscript, we review the available literature on the role of cortisol as a physiological marker for improvement with regards to mindfulness practice, and make recommendations for future study designs.