<i>Background:</i> Orange allergens are virtually unknown, in spite of the large consumption of this fruit. Germin-like proteins, together with vicilins and legumins, form the cupin superfamily of plant proteins, which includes many seed allergens. <i>Methods:</i> Twenty-nine patients with allergy to oranges were studied. A major IgE-binding protein from orange extracts was isolated by means of a two-step cation-exchange chromatographic protocol. The allergen was characterized by N-terminal amino acid sequencing and MALDI analysis, and its reactivity explored by specific IgE determination in individual sera, ELISA inhibition assays and in vivo skin prick tests (SPT). Chemical deglycosylation of the purified allergen was achieved by trifluoromethylsulfonate acid treatment. <i>Results:</i> The 24-kDa purified allergen, designated Cit s 1, was identified as a germin-like glycoprotein, based on its N-terminal amino acid sequence, molecular size and recognition by rabbit anti-complex N-linked glycan antibodies. Specific IgE to Cit s 1 was detected in 62% of 29 individual sera from orange-allergic patients, whereas positive SPT responses to the purified allergen were obtained in only 10% of such patients. Deglycosylation of Cit s 1 resulted in a loss of its IgE-binding capacity. Moreover, the unrelated plant glycoprotein horseradish peroxidase inhibited over 70% the IgE-binding to Cit s 1. <i>Conclusions:</i> Over 60% of patients with allergy to oranges show specific IgE to Cit s 1. However, the purified allergen exerts a low in vivo reactivity. Complex N-linked glycans seem to play a prominent role in the IgE-binding capacity of Cit s 1. This characteristic of Cit s 1, as well as of other orange glycoproteins, could lead to false positives if the diagnosis of allergy to oranges is mainly based on in vitro specific IgE determination.