Cardiovascular diseases remain the leading cause of death in most countries, including Russia. Non-pharmacological modalities intended for the primary prevention of cardiovascular disease including hypertension and atherosclerosis currently acquire special significance. The objective of the present study was to develop a system of methods for early diagnostics, prevention and treatment of the preclinical stages of atherosclerosis and hypertension Another objective was to estimate the effectiveness of these methods. A total of 310 patients at risk of arterial hypertension and atherosclerosis or with pre-clinical stages of these conditions were examined during a two year observation period. The system of early diagnosis and non-pharmacological primary prevention of cardiovascular disease was developed and evaluated using climatotherapeutic and physiotherapeutic methods in combination with and personalized dietary therapy, hypoxic-hypercapnic factors and educational programs. The study has demonstrated that the proposed system allowed to significantly (p<0,05) reduce cardiovascular morbidity. The patients of the main group experienced the reduction of abdominal obesity and blood pressure along with the improvement of the blood lipid profile and other indicators. These parameters remained unaltered in the patients comprising the control group. In the main group, the incidence of coronary heart disease and hypertension was 62.5% and 81.25% lower respectively than in the control group.