Use of a mixture of Nafion and glutaraldehyde as new immobilization matrix was described. The percentage of Nafion was optimized to prevent denaturation of horseradish peroxidase enzyme after its crosslinkage with glutaraldehyde on electro-synthesized polypyrrole surface. Topographic study by Atomic Force Microscopy (AFM) shows that the enzyme seems to have been introduced inside the ionic cluster of Nafion. The characterization of the resulting bio-interfaces by UV-vis and FT-IR shows that the intra-crosslinkage phenomena caused by the use of glutaraldehyde can be eliminated by the optimization of the concentration of Nafion additive. The secondary structure contents of native and immobilized enzyme were analyzed by a Gaussian curve fitting of the respective FT-IR spectra in the amide I region. Immobilized enzyme presented notable increasing percentages of globular and short helical structure compared with native enzyme. This indicates that immobilized enzyme was folded which is in accordance with AFM studies and supports the enzyme entrance inside ionic clutter of Nafion. Thanks to synergic effects of the polypyrrole conducting polymer and the perfluorosulfonic acid polymer Nafion, HRP enzyme was immobilized in its "native" state, the resulting biosensor was able to sense peroxide without any chemical mediator and can be categorized as third generation. (C) 2011 Elsevier B.V. All rights reserved.