The origins of several of the differentiated cell lineages of the advanced sea urchin embryo are well defined. Cytological application of molecular probes to three lineages, those responsible for the formation of the skeleton, the gut, and the aboral ectodermal wall of the late embryo, has demonstrated expression of lineage-specific genes long before overt morphological differentiation. These observations lead to useful generalizations regarding the processes of gene regulation that underlie the molecular biology of cell lineage specification in the embryo.