In this study, the in vivo biocompatibility was evaluated by using conventional ionomer cements modified with Chlorhexidine (CHX) in different time intervals. In total, 105 male Wistar rats were randomized into seven groups: control, groups M, M10, M18 and groups RL, RL10, RL18 (M-Meron and RL-RivaLuting, and added CHX-10% and CHX-18%, respectively). Histological analyses of inflammatory infiltrate and collagen fibers, and immunohistochemistry of CD68+ for macrophages (MOs) and multinucleated giant cells (MGCs) were performed. Data were analyzed using the Kruskal-Wallis and Dunn (p< .05) tests. Intense inflammatory infiltrate was demonstrated in Group Riva CHX-18% within 7 and 15 days (p< .05), without differences after 30 days. For collagenization, healing of the groups was compatible with that of control in 15 and 30 days (p> .05). Immunomarking of CD68+ was more significant in the groups with higher concentration of CHX. There was significant difference in quantity of MGCs in groups with 18% CHX, Meron (p= .001) in 7 days, and in Riva at 30 days (p= .001). Significant difference was also found in quantities of MOs in Groups Meron and Riva in 7 days (p= .001), and only in Riva at 15 and 30 days (p= .001). The cements with addition of CHX demonstrated biocompatibility with tissues. Riva CHX-18% had the most effect on cells of the inflammatory process but showed satisfactory tissue repair. RESEARCH HIGHLIGHTS: The concentration of 18% chlorhexidine was shown to be biocompatible with tissues; the slow release of chlorhexidine by the cements could significantly prolong its antibacterial effect on the oral medium.