The analysis of gene expression patterns in the neural plate and neural tube of the embryonic mouse forebrain shows that, at its earliest stages, the neuroepithelium is subdivided into molecularly distinct domains. Here, and in previous publications, we provide evidence that the patterns of gene expression can be related to primary morphogenetic processes that organize the histological primordia of the embryonic central nervous system into longitudinal and transverse domains. Longitudinal domains are generated by dorsoventral patterning signals produced by the axial mesendoderm and nonneural ectoderm. Transverse domains (proneuromeres and neuromeres) expressing distinct combinations of genes are present in the neural plate and neural tube.