β-Lactoglobulin (β-LG) is one of the cow's major milk proteins and the most abundant whey protein. This globular protein of about 18 kDa is folded, forming a β-barrel (or calyx) structure. This structure is stabilized by two disulfide bonds and can be altered by heating above 65 °C. β-LG is also one of the major allergens in milk. Heating is one of the most common technologic treatments applied during many milk transformations. During heating in the presence of reducing sugars, β-LG is also submitted to the Maillard reaction, which at the first stage consists of the covalent fixation of sugars on the ε-amino groups of lysyl residues. The following steps are condensation and polymerization reactions leading to the formation of melanoidins (brown pigments). Despite the frequency of use of heating during milk transformation, the effects of heat-induced denaturation and of glycation of β-LG on its recognition by IgE from cow's milk allergy (CMA) patients are not fully understood. The objectives of our work were to evaluate the effect of heat-induced denaturation of bovine β-LG on binding of IgE from CMA patients and to determine the effect of moderate glycation on the degree of recognition by IgE. We showed that heat-induced denaturation (loss of tertiary and secondary structures) of β-LG is associated with weaker binding of IgE from CMA patients. It was also shown that moderate glycation of β-LG in early stages of Maillard reaction has only a small effect on its recognition by IgE, whereas a high degree of glycation has a clear “masking” effect on the recognition of epitopes. This demonstrates the importance of ε-amino groups of lysines in the definition of epitopes recognized by IgE.