The objectives of this study were to investigate changes in the activity and expression of matrix metalloproteinase (MMP)-2 and MMP-9 in permanent teeth with or without exposure to radiotherapy, and the role of proteinase inhibitors in their inactivation. In situ zymography and immunofluorescence assays were performed to evaluate the activity and expression of two key gelatinases (MMP-2 and MMP-9) in sections of permanent molars, assigned to irradiated and nonirradiated subgroups. Dental fragments were exposed to radiation at a dose of 2 Gy fractions for 5 consecutive days until a cumulative dose of 60 Gy was reached. To evaluate the effect of protease inhibitors on MMPs, teeth were immersed in 0.5 mL of 0.12% chlorhexidine digluconate (CHX), 0.05% sodium fluoride (NaF), 400 μM polyphenol epigallocatechin-3-gallate (EGCG), or distilled water (control) for 1 h. Fluorescence in the dentinoenamel junction (DEJ) was evaluated in 3 areas of the tooth: cervical, cuspal, and pit. These regions were photographed using a fluorescence microscope at 1.25× and 5× magnifications. Results were analyzed using the D’Agostino-Person normality test, and the Kruskal-Wallis, Dunn, and Wilcoxon tests for intergroup and paired comparisons (α = 0.05). The fluorescence intensity/mm2 in the DEJ at the three regions studied was higher in the irradiated teeth (p < 0.05) than in the nonirradiated teeth, revealing regions of expression of MMP-2 and MMP-9 by immunofluorescence. Postradiotherapy treatment with different solutions (CHX, NaF, and EGCG) led to lower fluorescence intensity/mm2 in irradiated teeth than in the control group (distilled water; p < 0.05), as a result of MMP inactivation. In conclusion, irradiation increased gelatinase activity in all regions of the DEJ. Treatment with 0.12% CHX, 0.05% NaF, and 400 μM polyphenol EGCG postradiotherapy inactivated enzyme activity.