Background: Matrix metalloproteinases (MMPs) are proteolytic enzymes involved in degradation of the extracellular matrix. MMP-8 has been reported to be involved in the degradation of collagen in progression of dental caries. MMP-13 was found to be expressed in both normal and caries pulp, implying its involvement in the pathogenesis of dental caries. Methods: Four extracted teeth were used. They were categorized into four grades according to caries progression. Three sections were prepared from each separated crown and root. Immunofluorescence of the FITC of the MMP-8 and 13 in coronal and radicular dentin was analyzed by confocal microscopy. Results: Immunofluorescence signals that were indicative of MMP-8 were observed both in radicular and coronal dentin in the sound, C1 and C3 carious teeth. In C2 carious teeth, immunofluorescence signals that were indicative of MMP-8 were observed only in radicular dentin. Immunofluorescence signals that were indicative of MMP-13 were observed both in radicular and coronal dentin in the sound teeth. In C1, C2 and C3 carious teeth, immunofluorescence signals that were indicative of MMP-13 were not observed both in radicular and coronal dentin. Conclusion: Immunofluorescence signals revealed that MMP-8 and 13 were present in coronal and radicular dentin, and was differently expressed as caries progressed.