Although thermal treatments are beneficial for the preservation and safety of milk, they can also alter its immunogenic activity by affecting its protein components. To achieve precise results, it is essential to identify the specific proteins that cause food allergies. Therefore, investigating the possible alterations of cow's milk proteins (CMPs) resulting from thermal treatments is necessary. In this study, the Fourier transform infrared spectroscopy (FTIR) technique was used to analyze the effect of UHT thermal treatment on the secondary structures of milk casein. Using the second derivative, six characteristic peaks were identified in the Amide I region, ranging from 1700 to 1600 cm-1. It was found that thermal treatments produce shifts in absorption peaks, indicating changes in protein conformation and possibly in allergenic activity. These shifts were clearly identified in the first characteristic peak of samples M8 and M9, from 1621 to 1600 cm-1. The results suggest that thermal treatments may promote protein aggregation by increasing beta turns and reducing beta sheets and alpha helices, which could enhance the allergenic potential of the proteins and facilitate the formation of complexes between different milk proteins, such as beta-lactoglobulin and kappa-casein. Further studies are needed to experimentally validate the allergenic activity of proteins modified by thermal treatments, as only an analytical method (FTIR) was used to evaluate the secondary structures of the proteins.