The neural plate consists of neuroepithelial cells that serve as progenitors for the mature central nervous system. The neural plate is a highly regionalized structure, harboring neural progenitors with different programs of differentiation, due to signaling or intrinsic differences in their differentiation potential. In the frog neural plate, neural progenitors located in the deep or superficial layer differ in their ability to contribute to early (primary) neurogenesis but intercalate during neurulation. In order to understand the origins and mechanisms of this progenitor heterogeneity, it is necessary to be able to follow directly the fate of different progenitors. Here, we describe a fate mapping method, which is based on homotopic and homochronic grafts of labeled tissue to unlabeled, or differentially labeled, hosts. This method can be combined with immunohistochemical analysis with cell type specific markers, thus allowing one to determine the contribution that each early progenitor type makes to the differentiated nervous system. Such labeling can also be used to examine the morphogenetic movements that take place during neurulation.