The concept of autonomic regulation (aR) reflects the relevance of the function of different autonomic systems for health. aR can be captured by questionnaires. We differentiate between a trait or constitutional aR questionnaire version including 12 (short-version) or 18 items, respectively, with three subscales (orthostatic-circulatory, rest/activity and digestive regulation), and an 18-item state aR questionnaire on the preceding week with four subscales (rest/activity, orthostatic-circulatory, thermo- and digestive regulation). The validated questionnaires show satisfying to good reliability and robust validity with clear construct validity. In this article, we summarized the actually available literature on aR and the use of aR questionnaires in clinical and observational studies. We described the relationship of high aR with health and in case of low aR or loss of regulation with disease and functional disorder in the three (four) different subscales and functional systems, such as rest/activity, orthostatic-circulatory or digestive regulation (thermoregulation) with the consecutive therapeutic need. Finally, we gave perspectives of its further application in clinical research.