Abstract β-Conglycinin is a functional glycoprotein and one of the most important soybean allergens. The aim of the present research was to investigate the role of the N-glycans moieties of β-conglycinin on its in vitro immunoreactivity. The soy allergen was obtained by isoelectric precipitation from commercial soy protein isolate and was enzymatically deglycosylated by PNGase F (Peptide N-Glycosidase F EC 3.5.1.52). In order to optimize deglycosylation conditions different reaction times and allergen concentrations were tested. The extent of deglycosylation was estimated by SDS–PAGE, CZE, RP-HPLC, and MALDI-TOF MS analyses, which provided information related to changes in protein structure. The antigenicity of both native β-conglycinin and its deglycosylated form was evaluated by western-blotting and indirect ELISA employing polyclonal rabbit anti-soybean sera and horseradish peroxidase-labeled goat anti-rabbit IgG while the in vitro allergenicity was assessed by means of indirect competitive inhibition ELISA employing human sera (IgE) of soy allergics. β-Conglycinin was effectively deglycosylated by PNGase F. Data on immunological tests suggested that glycosyl moieties forming this glycoprotein might be involved in its immunoreactivity.