The diagnosis of food intolerance is tricky due to the different etiologies of adverse reactions. There is also a lack of clear rules for interpreting alternative tests used to diagnose these problems. The analyses of IgG4 concentration in serum or cytotoxic tests became the basis of elimination diets. However, it can result in nutritional deficiencies and loss of tolerance to eliminated foods. Our study aimed to assess the necessity of food elimination in four cases with food intolerance symptoms based on alternative diagnostic tests. Four patients without food allergies, who manifested diverse clinical symptoms after food, were presented due to the following factors: clinical history, diagnostic tests, elimination diet, and filaggrin gene (FLG) mutation. It was found that higher IgG4 levels against foods and higher cytotoxic test values are not clinically relevant in each of the studied individuals. They should not be decisive for the elimination of food products. The study of FLG-SNVs revealed the association of some clinical symptoms in patients with hypersensitivity to several food allergens and reported genetic variants in the FLG gene.