Our review demonstrates that the whole embryo culture system established by New and his colleagues, in combination with beneficial fluorescent dye cell-tracing techniques, has greatly contributed to many advancements in the field of mammalian craniofacial embryology, especially with regard to elucidating the developmental behavior of cephalic crest cells. In addition, based on recent results, further combining whole embryo culture with mandibular organ culture methods has allowed us to trace cranial crest cells for a much longer developmental period, i.e., presently up to the cap stage in odontogenesis.