A major issue in developmental biology is to determine how time and position-restricted instructions are signaled and received during morphogenesis of different phenotypes, of which tooth, Meckel's cartilage and tongue formation are classical examples. It is now evident that a hierarchy of growth factors and their downstream transcription factors regulate the timing, sequence and position of cells and tissues in forming different phenotypes during embryogenesis. Here we report the development of an early mandibular organ culture model. Explants of E8 and E9 first branchial arch were cultured and produced mandibular processes with cap stage tooth formation, Meckel's cartilage and tongue development. In tandem, vital dye (Dil) labeling studies confirmed that rhombomeres 1-4 give rise to craneal neural crest (CNC) cells which emigrate from the neural fold to the forming maxillary and mandibular arches. Furthermore, we have tested the feasibility of investigating the regulation of different phenotypes within the first branchial arch by a transcription factor using this early mandibular organ culture model. Lymphoid enhancing factor 1 (Lef1), a transcription factor, has been implicated to regulate tooth formation in vivo. We have analyzed the expression of Lef1 and studied the biological effects of Lef1 on E8 embryonic mouse first branchial arch explants in organ culture. Collectively, these results demonstrate that first branchial arch explant model is suitable for studies of rhombencephalic crest cell fate during mandibular morphogenesis and can be used as a model with direct access to investigate the molecular mechanism in regulating first branchial arch morphogenesis.