Effects of capping agents on two waves of apoptosis during pulp wound healing were examined. After cavity preparation of rat molars, cavities were filled with calcium hydroxide, zing oxide eugenol cement, or 4-META/MMA-TBB resin (4MMT) and some were unfilled. One hour or 1 day after filling, we examined the distribution and the number of apoptotic cells by terminal deoxynucleotidyl transferase-mediated labeling (TUNEL) assay. One hour after filling, there were no differences in distribution patterns or the number of apoptotic odontoblasts among the four groups. One day after filling, we found differences in distribution patterns and the number of apoptotic pulp cells among the four groups. Especially in the 4MMT group, the distribution pattern of apoptotic cells was more broadly spread, and the number of apoptotic cells was significantly larger than those of other groups. These results suggest that capping agents may have an effect on pulp apoptosis and that 4MMT may actively induce apoptosis during pulp wound healing.