We investigated the pulpal response to direct pulp capping in rat molar teeth using mineral trioxide aggregate (MTA) and calcium hydroxide (CH). A palatal cavity was prepared in rat maxillary molar teeth. Either MTA or CH was placed on the exposed pulp and all cavities were restored with composite. Rats were sacrificed for histological evaluation after 12 hours and at 2, 7, 14 and 21 days. In both the MTA and CH groups, reparative dentin formation was clearly observed on histology after 14 days. The MTA-capped pulps were found to be mostly free from inflammation, and hard tissue of a tubular consistent barrier was observed. In contrast, in CH-capped teeth, excessive formation of reparative dentin toward residual pulp was evident. The pulpal cell response beneath the reparative dentin layer was examined by immunofluorescence using antibodies against DSP. After 2 days, a few DSP immunopositive cells, most of which showed a cuboidal shape, appeared beneath the predentin layer. At 7 days, DSP-immunopositive cells with columnar odontoblast-like cells were seen beneath the newly formed hard tissues. At 14 and 21 days, DSP was more abundant in the vicinity of the odontoblastic process along the dentinal tubules than in the mineralized reparative dentin. The CH group showed strong expression patterns in terms of DSP immunoreactivity. Our results thus indicate that MTA may be a more effective pulp capping material as it induces the differentiation of odontoblast-like cells and the formation of reparative dentin without the loss of residual pulp functions.