To test the hypothesis that a commercial solution of 5% NaOCl produces structural and molecular alterations in the collagen and glycosaminoglycans of mineralized and demineralized dentin, radicular segments from human teeth were treated with 5% NaOCl or 2 min at room temperature. As a control, distilled water replaced NaOCl. The experimental and control specimens were processed for indirect immunofluorescence by using antitype I collagen and antichondroitin sulfate antibodies. Tissue sections were morphometrically analyzed. A single exposure for 2 min to a 5% NaOCl solution produced a drastic loss of immunoreactivity in the dentin surface for both antibodies that were used in demineralized specimens. A narrow and irregular band of fluorescence loss was detected in mineralized-dentin segments when anticollagen antibodies were used. The results of this study suggest that 5% NaOCl induces alterations in dentin collagen and glycosaminoglycans and show the protective role of hydroxyapatite on organic matrix stability.