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Purpose: This study was conducted to study the influence of protein structure on the immunogenicity in wild-type and immune tolerant mice of well-characterized degradation products of recombinant human interferon alpha2b (rhIFNalpha2b)., Methods: RhIFNalpha2b was degraded by metal-catalyzed oxidation (M), cross-linking with glutaraldehyde (G), oxidation with hydrogen peroxide (H), and incubation in a boiling water bath (B). The products were characterized with UV absorption, circular dichroism and fluorescence spectroscopy, gel permeation chromatography, reverse-phase high-pressure liquid chromatography, sodium dodecyl sulfate polyacrylamide gel electrophoresis, Western blotting, and mass spectrometry. The immunogenicity of the products was evaluated in wild-type mice and in transgenic mice immune tolerant for hIFNalpha2. Serum antibodies were detected by enzyme-linked immunosorbent assay or surface plasmon resonance., Results: M-rhIFNalpha2b contained covalently aggregated rhIFNalpha2b with three methionines partly oxidized to methionine sulfoxides. G-rhIFNalpha2b contained covalent aggregates and did not show changes in secondary structure. H-rhIFNalpha2b was only chemically changed with four partly oxidized methionines. B-rhIFNalpha2b was largely unfolded and heavily aggregated. Nontreated (N) rhIFNalpha2b was immunogenic in the wild-type mice but not in the transgenic mice, showing that the latter were immune tolerant for rhIFNalpha2b. The anti-rhIFNalpha2b antibody levels in the wild-type mice depended on the degradation product: M-rhIFNalpha2b > H-rhIFNalpha2b approximately N-rhIFNalpha2b >> B-rhIFNalpha2b; G-rhIFNalpha2b did not induce anti-rhIFNalpha2b antibodies. In the transgenic mice, only M-rhIFNalpha2b could break the immune tolerance., Conclusions: RhIFNalpha2b immunogenicity is related to its structural integrity. Moreover, the immunogenicity of aggregated rhIFNalpha2b depends on the structure and orientation of the constituent protein molecules and/or on the aggregate size.