The invention relates to medicine, and specifically to personalized diet therapy, in particular to the creation of individual meal plans on the basis of DNA analysis. To this end, the causes of overweight and food intolerance are specified by studying the polymorphism of genes selected from among LCT, PPARG, ADRB2, FABP2 and TCF7L2, and the haplotype of HLA-DQ is determined. In addition, a personalized menu and dietary recommendations are compiled according to the polymorphic variants identified. The method provides effective treatment and prevention of overweight and food intolerance by selecting an appropriate diet without the use of pharmacological preparations. The method can be used in the practice of dietitians, endocrinologists and gastroenterologists to treat and prevent obesity and type 2 diabetes and to identify the fundamental causes of food intolerance.