Matrix metalloproteinases (MMPs) and their specific tissue inhibitors (TIMPs) participate into extracellular matrix degradation in physiological and pathological conditions. We hypothesized that MMP expression in pulp tissue changes in response to caries attack and investigated the gene expression profiles of MMPs and TIMPs in pulp tissue of sound and carious teeth with cDNA microarray. cDNA microarray demonstrated an extremely high MMP-13 (collagenase-3) mRNA expression in pooled pulp samples of sound and carious teeth, with less pronounced expression of MMP-16 (MT3-MMP) and TIMP-1. Real-time quantitative polymerase chain reaction of individual pulp samples revealed a wide range of the MMP-13 expression level between pulp samples with possible downregulation of MMP-13 expression during caries progression. Western blot and immunohistochemical staining confirmed the presence of MMP-13 with no observable differences between sound and carious teeth pulp tissues. The results reveal that MMP-13 is expressed and synthesized in pulp tissue, an interesting feature considering the very limited expression of MMP-13 in normal adult tissues. Further studies with a larger sample size are needed to clarify the changes in MMP-13 expression during caries progression.