Runx2/Cbfa1 is an essential transcription factor for osteoblast differentiation and bone formation. Runx2/Cbfa1 knockout mice showed both a complete lack of ossification and the developmental arrest of tooth germ. We here report Runx2/Cbfa1 isoform-type specific functional roles in the development of tooth germ by the administration of antisense phosphorothioate oligodioxynucleotides (S-ODNs) into cultured mouse mandibles. The administration of type II/III Runx2/Cbfa1 antisense S-ODNs into the culture media resulted in an arrest of tooth germ growth at the bud-like stage in cultured mandible taken from the 11-day-old embryos, while also causing the inhibition of the differentiation of odontogenic cells into ameloblast and odontoblast in cultured tooth germs taken from the 15-day-old embryos. The expression of dentin matrix protein 1, dentin sialophosphoprotein, amelogenin, and ameloblastin was shown to be markedly suppressed in cultured tooth germ by the semi-quantitative RTPCR. Meanwhile, no developmental arrest of tooth germ, no inhibition of gene expression, or differentiation of odontogenic cells was observed in samples treated with the type I Runx2/Cbfa1 antisense S-ODNs. The same findings were also observed in either the control or the sense and random sequence S-ODNs-treated samples. These data indicate that the type II/III Runx2/Cbfa1 isoform is closely related to the development and differentiation of tooth germ. (c) 2005 Elsevier Inc. All rights reserved.