BACKGROUND: Thioredoxins are cross-reactive allergens involved in the pathogenesis of atopic eczema and asthma. Cross-reactivity to human thioredoxin can contribute to the exacerbation of severe atopic diseases. METHODS: Human thioredoxin, Asp f28 and Asp f29, two thioredoxins of Aspergillus fumigatus, and thioredoxin of Malassezia sympodialis were cloned and produced as recombinant proteins. Allergenicity and cross-reactivity to thioredoxins in allergic bronchopulmonary aspergillosis patients were assessed by enzyme-linked immunosorbent assay (ELISA), inhibition ELISA, immunoblot analysis, proliferation assays and skin tests. Molecular homology modelling was used to identify conserved, surface-exposed amino acids potentially involved in immunoglobulin E (IgE)-binding. RESULTS: All thioredoxins, including the human enzyme, bind IgE from patients with allergic bronchopulmonary aspergillosis and induce allergen-specific proliferation in peripheral blood mononuclear cells and positive skin reactions in thioredoxin-sensitized patients. Inhibition experiments showed that the thioredoxins are cross-reactive indicating humoral immune responses based on molecular mimicry. To identify structural surface elements involved in cross-reactivity, the three-dimensional structures were modelled based on solved thioredoxin structures. Analysis of the molecular surfaces combined with sequence alignments allowed identification of conserved solvent exposed amino acids distantly located in the linear sequences which cluster to patches of continuous surface areas. The size of the surface areas conserved between human and fungal thioredoxins correlates well with the inhibitory potential of the molecules in inhibition ELISA indicating that the shared amino acids are involved in IgE-binding. CONCLUSIONS: Conserved, solvent exposed residues shared between different thioredoxins cluster to continuous surface regions potentially forming cross-reactive conformational B-cell epitopes responsible for IgE-mediated cross-reactivity and autoreactivity.