The focus of this study was to evaluate the antimicrobial, mechanical properties and biocompatibility of glass ionomer (GICs) modified by Chlorhexidine (CHX). For biocompatibility, 105 male Wistar rats were used, divided into 7 groups (n=15): Group C (Control,Polyethylene), Groups M, M10, M18, and Groups RL, RL10, RL18 (M-Meron and RL-Riva Luting: conventional, and modified with 10%, and 18% CHX, respectively). The tissues were analyzed under optical microscope for different cellular events and time intervals. Antibacterial effect and Shear Bond Strength Test (SBST) were also analyzed. Biocompatibility was analyzed by the Kruskal-Wallis and Dunn tests; SBST one-way ANOVA and Tukey test (P<0.05). For the antibacterial effect, the Kruskal-Wallis and Friedman, followed by Dunn (P<0.05) tests were used. Morphological study of the tissues showed inflammatory infiltrate with significant differences between Groups C and RL18, in the time intervals of 7(P=0.013) and 15(P=0.032) days. The antimicrobial effects of the cements was shown to be CHX concentration-dependent (P=0.001). The SBST showed no significant difference between the Groups of Meron cement (P=0.385), however, there was difference between Group RL and Groups RL10 and RL18 (P=0.001). The addition of CHX did not negatively influence the SBST. Meron-CHX-10% was the most biocompatible, and Riva-CHX-18% had more influence on the inflammatory process and presented slower tissue repair.