The body tail is a characteristic trait of vertebrates, which endows the animals with a variety of locomotive functions. During embryogenesis, the tail develops from the tail bud, where neural and mesodermal tissues make a major contribution. The neural tube in the tail bud develops by the process known as secondary neurulation (SN), where mesenchymal cells undergo epithelialization and tubulogenesis. These processes contrast with the well known primary neurulation, which is achieved by invagination of an epithelial cell sheet. In this study we have identified the origin of SN-undergoing cells, which is located caudo-medially to Hensen's node of early chicken embryo. This region is distinctly fate-mapped from tail-forming mesoderm. The identification of the presumptive SN region has allowed us to target this region with exogenous genes using in ovo electroporation techniques. The SN-transgenesis has further enabled an exploration of molecular mechanisms underlying mesenchymal-to-epithelial transition during SN, where activity levels of Cdc42 and Rac1 are critical. This is the first demonstration of molecular and cellular analyses of SN, which can be performed at a high resolution separately from tail-forming mesoderm.