The molecular mechanisms governing the decision between molariform and incisiform patterns of rodent dentition are not yet known. Transcription factors are regulators of regionally specific morphogenesis and key co-ordinators of gene activity during developmental processes. Here, we analysed the expression of several transcription factors during mouse tooth development. Otlx2/Rieg is a homeobox gene involved in Rieger syndrome, a human disorder characterized by dental hypoplasia. Otlx2/Rieg expression distinguishes stomatodeal epithelium well before tooth initiation, and thereafter its expression becomes restricted to the epithelia of both molar and incisor primordia. The recently identified homeodomain transcription factor Barx1 is first expressed in mesenchyme of the first branchial arch, but during advanced developmental stages the gene is exclusively expressed in the mesenchyme of molar primordia. Finally, the Sry-related transcription factor Sox9 is expressed in epithelial components and to a lesser degree in condensed mesenchyme of the developing teeth. These results suggest that Otlx2/Rieg, Barx1, and Sox9 participate in the hierarchical cascade of factors involved in the regulation of tooth morphogenesis.