Background:  Non‐specific lipid transfer proteins (LTPs) are involved in allergy to fresh and processed fruits. We have investigated the effect of thermal treatment and glycation on the physico‐chemical and IgE‐binding properties of the LTP from apple (Mal d 3). Methods:  Mal d 3 was purified from apple peel and the effect of heating in the absence and presence of glucose investigated by CD spectroscopy, electrospray and MALDI‐TOF mass spectrometry. IgE reactivity was determined by RAST and immunoblot inhibition, SPT and basophil histamine release test. Results:  The identity and IgE reactivity of purified Mal d 3 was confirmed. Mild heat treatment (90°C, 20 min) in the absence or presence of glucose did not alter its IgE reactivity. More severe heat treatment (100°C, 2 h) induced minor changes in protein structure, but a significant decrease in IgE‐binding (30‐fold) and biological activity (100‐ to 1000‐fold). Addition of glucose resulted in up to four glucose residues attached to Mal d 3 and only a 2‐ and 10‐fold decrease of IgE‐binding and biological activity, respectively. Conclusions:  Only severe heat treatment caused a significant decrease in the allergenicity of Mal d 3 but glycation had a protective effect. The presence of sugars in fruits may contribute to the thermostability of the allergenic activity of LTP in heat‐processed foods.