BACKGROUND: Tooth development is known to be mediated by the cross-talk between signaling pathways, including Shh, Fgf, Bmp, and Wnt. MicroRNAs (miRNAs) are 19- to 25-nt noncoding small single-stranded RNAs that negatively regulate gene expression by binding target mRNAs, which is believed to be important for the fine-tuning signaling pathways in development. To investigate the role of miRNAs in tooth development, we examined mice with either mesenchymal (Wnt1Cre/Dicer(fl/fl)) or epithelial (ShhCre/Dicer(fl/fl)) conditional deletion of Dicer, which is essential for miRNA processing. RESULTS: By using a CD1 genetic background for Wnt1Cre/Dicer(fl/fl), we were able to examine tooth development, because the mutants retained mandible and maxilla primordia. Wnt1Cre/Dicer(fl/fl) mice showed an arrest or absence of teeth development, which varied in frequency between incisors and molars. Extra incisor tooth formation was found in ShhCre/Dicer(fl/fl) mice, whereas molars showed no significant anomalies. Microarray and in situ hybridization analysis identified several miRNAs that showed differential expression between incisors and molars. CONCLUSION: In tooth development, miRNAs thus play different roles in epithelium and mesenchyme, and in incisors and molars.