This study investigates the degradation of collagen matrices in acid-etched dentin over time, focusing on the role of host-derived enzymes, particularly matrix metalloproteinases (MMPs), in the process. The research aimed to determine whether acid-etched dentin matrices can be degraded by dentin-derived proteolytic enzymes in the absence of bacterial colonization. The null hypothesis was that there would be no difference in the degradation of acid-etched dentin matrices stored in artificial saliva, artificial saliva with proteolytic enzyme inhibitors, or non-aqueous mineral oil. Twenty-seven non-carious human third molars were used to prepare demineralized collagen matrices (DCMs) by etching the tooth surfaces with a silica-free 32% phosphoric acid gel. The specimens were divided into three groups: experimental (stored in artificial saliva with sodium azide), control 1 (stored in pure mineral oil), and control 2 (stored in artificial saliva with proteolytic enzyme inhibitors). The DCMs were examined using transmission electron microscopy (TEM) at 24 hours, 90 days, and 250 days. The results showed that DCMs in the experimental group were almost completely destroyed after 250 days, while those in the control groups remained intact. This indicated that hydrolytic degradation of denuded collagen fibrils occurs in the absence of bacterial colonization. Functional enzyme analysis of dentin powder revealed low levels of collagenolytic activity, which was inhibited by protease inhibitors or 0.2% chlorhexidine. The study hypothesized that collagen degradation occurs over time due to the slow release of host-derived MMPs. The findings suggest that host-derived MMPs, particularly MMP-2, play a significant role in the degradation of collagen matrices in dentin, contributing to the pathogenesis of dentin caries and periodontal disease. The study also highlights the importance of preventing collagen degradation in resin-dentin bonds to improve their longevity. The results indicate that MMP inhibition may be a promising approach to prevent collagen degradation in resin-dentin bonds, with chlorhexidine showing potential as an MMP inhibitor.This study investigates the degradation of collagen matrices in acid-etched dentin over time, focusing on the role of host-derived enzymes, particularly matrix metalloproteinases (MMPs), in the process. The research aimed to determine whether acid-etched dentin matrices can be degraded by dentin-derived proteolytic enzymes in the absence of bacterial colonization. The null hypothesis was that there would be no difference in the degradation of acid-etched dentin matrices stored in artificial saliva, artificial saliva with proteolytic enzyme inhibitors, or non-aqueous mineral oil. Twenty-seven non-carious human third molars were used to prepare demineralized collagen matrices (DCMs) by etching the tooth surfaces with a silica-free 32% phosphoric acid gel. The specimens were divided into three groups: experimental (stored in artificial saliva with sodium azide), control 1 (stored in pure mineral oil), and control 2 (stored in artificial saliva with proteolytic enzyme inhibitors). The DCMs were examined using transmission electron microscopy (TEM) at 24 hours, 90 days, and 250 days. The results showed that DCMs in the experimental group were almost completely destroyed after 250 days, while those in the control groups remained intact. This indicated that hydrolytic degradation of denuded collagen fibrils occurs in the absence of bacterial colonization. Functional enzyme analysis of dentin powder revealed low levels of collagenolytic activity, which was inhibited by protease inhibitors or 0.2% chlorhexidine. The study hypothesized that collagen degradation occurs over time due to the slow release of host-derived MMPs. The findings suggest that host-derived MMPs, particularly MMP-2, play a significant role in the degradation of collagen matrices in dentin, contributing to the pathogenesis of dentin caries and periodontal disease. The study also highlights the importance of preventing collagen degradation in resin-dentin bonds to improve their longevity. The results indicate that MMP inhibition may be a promising approach to prevent collagen degradation in resin-dentin bonds, with chlorhexidine showing potential as an MMP inhibitor.