Rapid technical developments have greatly facilitated noninvasive 24-hour recording of physiological signals at relatively low costs, including blood pressure, activity of the autonomic nervous system, respiratory behavior, and activity of the hypothalamic-pituitary-adrenocortical axis. Ambulatory noninvasive recordings can be used to study the baseline levels of these physiological variables as well as their reactivity to naturalistic stressors. Levels and reactivity can be compared across groups differing in exposure to risk factors (e. g., stress, genotypes) or used to sharpen the clinical profile of individual subjects (e. g., in panic or somatoform disorders). The focus of the current paper is on the importance of a priori choices in study design and data analysis strategies when ambulatory recording specifically targets the reciprocal relationship between physiological and psychological events. These choices are illustrated with ambulatory-assessed indices of the cardiac autonomic nervous system, blood pressure, respiration, and cortisol secretion.