The effect of TiO2 photocatalytic treatment on allergen proteins of pollen was evaluated. The allergenic activity and chemical composition of pollen allergenic extracts (PAE) of two species: Cupressus arizonica and Platanus hybrida acerifolia were characterised using three experimental techniques: scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and fluorescence spectrophotometry with the fluorescein diacetate probe (FDA). SEM and XPS experiments have shown that the total amount of organic matter of PAE decreased during the photocatalytic treatment. Furthermore, FDA fluorescence probe provided an indication that the enzymatic activity was completely inhibited after photocatalytic treatment. This result demonstrated evidences of the efficiency of the photocatalysis process in deactivation of pollen allergens.