Teeth develop via a reciprocal induction between the ectomesenchyme originating from the neural crest and the ectodermal epithelium. During complete formation of the tooth morphology and structure, many cells proliferate, differentiate, and can be replaced with other structures. Apoptosis is a type of genetically-controlled cell death and a biological process arising at the cellular level during development. To determine if apoptosis is an effective mechanism for eliminating cells during tooth development, this process was examined in the rat mandible including the developing molar teeth using the transferase-mediated dUTP-biotin nick labeling (TUNEL) method. The tooth germ of the mandibular first molar in the postnatal rat showed a variety of morphological appearances from the bell stage to the crown stage. Strong TUNEL-positive reactivity was observed in the ameloblasts and cells of the stellate reticulum. Odontoblasts near the prospective cusp area also showed a TUNEL positive reaction and several cells in the dental papilla, which are the forming pulp, were also stained intensively in this assay. Our results thus show that apoptosis may take place not only in epithelial-derived dental organs but also in the mesenchyme-derived dental papilla. Hence, apoptosis may be an essential biological process in tooth development.