During craniofacial development, cranial neural crest (NC)-derived mesenchymal cells migrate to pharyngeal arches and contribute extensively to neurons, Schwann cells, smooth muscle cells, osteoblasts, chondrocytes, and odontoblasts, forming maxillofacial structures. In vitro models using model organism cells, such as African clawed frog (Xenopus Laevis) and mouse (Mus Musculus), were developed to understand cellular and molecular mechanisms of cranial NC development. Recent studies using human embryonic stem cells (hESCs) and human-induced pluripotent stem cells (hiPSCs) have enabled the generation of human NC cells (NCCs) in vitro to provide insight into human NC development. Understanding molecular mechanisms underlying craniofacial development will contribute to develop novel embryotoxicity tests and to decrease the incidence of drug-induced congenital anomalies in the craniofacial region, such as cleft lip or cleft palate. Here, we review culture methods to derive NCCs in vitro from Xenopus presumptive ectoderm (animal caps), mouse embryonic stem cells (mESCs), and human pluripotent stem cells (hPSCs) and discuss how these in vitro models can be used to help clarify the mechanisms underlying craniofacial development and for developing embryotoxicity tests predicting drug-induced congenital anomalies in the craniofacial region.