65 patients aged from 31 to 89 years with a combination of acid-dependent, cardiovascular and endocrine diseases, who received various types of non-pharmacological physiotherapy after taking medicines, have been examined. Along with the common clinical research methods, the hardware and software complex «Reserves health — R» was used. The analysis with the help of modern statistical methods has shown the effectiveness of the rehabilitation methods on the background of positive dynamics of psychophysiological state. If heart rate variability indices — SDNN, CV (coefficient of variation), SI (stress index), as well as PARS (activity indicator of regulatory systems) — significantly differ from the norm in the initial state, which means a significant weakening of the adaptive capacity of the organism for a given syntropy, then the tendency to recover the sympathetic-vagal balance and a decrease in PARS from 5.3 ± 1.2 to 4.0 ± 0.5 p <0.01 is noted as a result of the rehabilitation. There was a significant decrease in the mean values of diastolic and systolic blood pressure, heart rate, and total peripheral vascular resistance. The conclusion has been made that there is a common nature of pathogenetic processes with the combination of the mentioned above diseases, which is proved with modern diagnostic methods. It is manifested in autonomic dysfunction with possible subsequent exacerbation of disease of the gastroenterological, cardiovascular and endocrinological systems, which requires the joint participation of specialists of the relevant fields for the management of such patients.