In the present study, the allergen in Siberian apricot (Prunus sibirica L.) kernel (SAK) was extracted, purified, and identified. The effect of high-pressure processing on the physiochemical property, structure, as well as the allergenicity of the allergen were determined. The changes in the molecular morphology and secondary structure of Siberian apricot kernels allergen (SAKA) after high hydrostatic pressure (HHP) processing were analyzed using atomic force microscopy and circular dichroism respectively. The immunoreactivity was evaluated by western blotting and indirect-binding enzyme-linked immunosorbent assays. Our result showed that after HHP processing, the intensity of a 40 kDa polypeptide band in SAKA was decreased. The immunoreactivity of SAKA was reduced to 72.74% +/- 1.09% after high pressure processing at 500 MPa for 900 s. The results of this study may provide important implications for identification of apricot kernel allergen as well as the development of apricot kernels foods and beverages with low level of allergenicity.