Abstract Nowadays, in the absence of a common doctrine and conceptual schemes, both of treatment and prevention of atopic diseases, we have practically uncontrolled growth of this pathology. This dead-end situation can only be changed, if there are clinical atopy biomarkers, thus making preventive therapy possible. The article presents the program development and implementation results for primary prevention of atopic dermatitis based on identified biomarkers. A preventive treatment method, based on the correction of intestinal microbiota through selective decontamination of opportunistic microflora using bacteriophages has been substantiated. The results of ten-year experience in secondary and primary prevention of atopic diseases are presented.