Pattern formation in the vertebrate ventral neural tube has been proposed to depend on the ability of notochord-derived signals to induce the differentiation of distinct cell types in a distance-dependent manner. To determine whether the distribution of early differentiating cell types in the ventral neural tube is consistent with the operation of such a mechanism in vivo, the early localization of Isl-1/2+ motor neurons in relation to HNF-3 beta+ floor plate cells has been investigated. In the most immature regions of the caudal spinal cord of early rat and chick embryos, an initial mixed distribution of cell types was detected that develops into a distribution characteristic of the final embryonic pattern where different cell types are found at distinct locations. In addition, a number of cells that coexpress both markers are detected within the floor plate. At later stages, coexpression is also detected in the hindbrain in the boundary region between HNF-3 beta+ ventricular cells and Isl-1/2+ motor neurons. The mixed distribution of early differentiating cells expressing HNF-3 beta and Isl-1/2 and the coexpression of these markers in single cells within the floor plate suggest that secondary cellular interactions are important in the generation of the final embryonic pattern of the neural tube.