The enamel knot (EK), located in the center of cap-stage tooth germs, is a transitory cluster of non-dividing epithelial cells, eventually linked to the outer dental epithelium by the enamel septum (ES). It might act as a signaling center providing positional information for tooth morphogenesis and could regulate the growth of tooth cusps through the induction of secondary signaling EKs. The EK undergoes apoptosis, which could constitute a mechanism whereby the signaling functions of this structure are terminated. Recently, we demonstrated the segregation of 5-bromo-2'-deoxyuridine (BrdU) negative inner dental epithelial (IDE) cells of the EK into as many individual groups of cells as cusps will form and suggested a morphogenetic role for these particular IDE cells. Using Z-VAD-fmk, a specific caspase inhibitor, apoptosis in the primary EK of first mouse lower cap-staged molars and lower incisors cultured in vitro was abrogated. No obvious histological alterations were observed in the incisors, whereas a prominent EK and an ES connecting the outer dental epithelium (ODE) and the BrdU negative IDE cells capping cusp L2 were observed in the molars. EK specific transcription (Shh, Msx-2, Bmp-2, Bmp-4) was down-regulated in the body of these structures with the exception of the associated IDE cells. In these experimental conditions, segregation of non-dividing transcriptionally active IDE cells occurred and a normal cusp pattern was expressed.