In a matter of a few days the murine tooth germ develops into a complex, mineralized, structure. Murine 30K microarrays were used to examine gene expression in the mandibular first molar tooth germs isolated at 15.5dpc and at 2DPN. Microarray results were validated using real-time RT-PCR. The results suggested that only 25 genes (3 without known functions) exhibited significantly higher expression at 15.5dpc compared to 2DPN. In contrast, almost 1400 genes exhibited significantly (P<0.015) higher expression at 2DPN compared to 15.5dpc, about half of which were genes with unknown functions. More than 50 of the 783 known genes exhibited higher than 10-fold increase in expression at 2DPN, amongst these were genes coding for enamel matrix proteins which were expressed several 100-fold higher at 2DPN. GO and KEGG analysis showed highly significant associations between families of the 783 known genes and cellular functions relating to energy metabolism, protein metabolism, regulation of cell division, cell growth and apoptosis. The use of bioinformatics analysis therefore yielded a functional profile in agreement with known differences in tissue morphology and cellular composition between these two stages. Such data is therefore useful in directing attention towards genes, or cellular activities, which likely are worthy of further studies as regards their involvement in odontogenesis.