Objective: The aim of the present work was to morphometrically evaluate collagen in carious lesions sealed with calcium hydroxide, adhesive systems, glass ionomer cement, and an antibacterial cement. Study design: Samples of infected and affected dentin were stained with Sirius Red (SR). The areas intensively stained with SR were delimited, and the percentage of these areas was measured by blind calibrated examiners. The mean results were subjected to the Kruskal-Wallis test. Results: The affected dentin sealed with Ca(OH)2 showed a better organization of the collagen in relation to the adhesive systems Prime & Bond (p= .0159) and Adhese (p<0.0001). The affected dentin sealed with Prime & Bond promoted better increase of organized collagen areas in relation to Adhese (p = 0.0004). The infected dentin sealed with glass ionomer cement (p = 0.0018) or antibacterial cement (p = 0.0004) brought a significant increase in the organized collagen areas. Conclusions: Ca(OH)2 is indicated to seal affected dentin and glass ionomer cement and antibacterial cement may be used for treatment of infected dentin. The addition of antibiotics did not influence the restoration of the infected dentin.