The objective of this in vivo study was to compare the expression of matrix metalloproteinases (MMP-2, MMP-8, MMP-9), type I collagen and bone sialoprotein (BSP) in infected dentin of primary teeth at baseline and after cavity sealing with glass ionomer cement. Dentin samples from 45 primary molars with deep and active carious lesions were collected before (baseline sample) and after cavity sealing (60-day sample). The samples were fixed, demineralized and processed for immunohistochemistry assays. Monoclonal antibodies were used for the localization of the cited antigens with an avidin-biotin method. Digital images of the sections were captured and analyzed with ImageJ software. The mean intensity of RGB channels in the images was obtained and compared using Student's t test (α = 0.05). The expression of the MMPs, type I collagen and BSP increased after sealing, but statistical differences were observed only for MMP-8, type I collagen and BSP. MMP-2 and MMP-9 were more concentrated around dentin tubules; MMP-8 and collagen showed strong expression throughout the organic matrix; BSP exhibited strong expression both in the matrix and around dentin tubules. The increased expression of the enzymes investigated 60 days after cavity sealing suggests that they are not related with disease progression but with the healing process of dentin.