The purpose of this study was to compare the biocompatibility of a new experimental root-end filling material, "Cold Ceramic" (CC), with mineral trioxide aggregate (MTA) in rats. After anaesthetising 10 rats and raising tissue flaps, tablets of the material were placed subcutaneously. Five rats were followed for seven days and five for 30 days. An incision without any implanted material was used as a control. Histological analyses were performed with regard to number, type and location of the inflammatory cells and type of surrounding tissue. Kruskal-Wallis and Mann-Whitney statistical tests were used. Comparing inflammatory reactions between the two experimental groups (MTA and CC) and the control group showed significant differences after seven days (p = 0.031). There were no significant differences between CC and MTA groups after seven days (p = 0.222) and after 30 days (p = 0.063). The results suggested that MTA and CC are both biocompatible. It appears that MTA induces less inflammatory response in short periods of observation, but CC may be more biocompatible for slightly longer periods.