Recent investigations into the roles of early regulatory genes, especially those resulting from mesoderm induction or first expressed in the gastrula, reveal a need to elucidate the developmental history of the cells in which their transcripts are expressed. Although fates both of the early blastomeres and of regions of the gastrula have been mapped, the relationship between the two sets of fate maps is not clear and the clonal origin of the regions of the stage 10 embryo are not known. We mapped the positions of each blastomere clone during several late blastula and early gastrula stages to show where and when these clones move. We found that the dorsal animal clone (A1) begins to move away from the animal pole at stage 8, and the dorsal animal marginal clone (B1) leaves the animal cap by stage 9. The ventral animal clones (A4 and B4) spread into the dorsal animal cap region as the dorsal clones recede. At stage 10, the ventral animal clones extend across the entire dorsal animal cap. These changes in the blastomere constituents of the animal cap during epiboly may contribute to the changing capacity of the cap to respond to inductive growth factors. Pregastrulation movements of clones also result in the B1 clone occupying the vegetal marginal zone to become the primary progenitor of the dorsal lip of the blastopore (Spemann's Organizer). This report provides the fundamental descriptions of clone locations during the important periods of axis formation, mesoderm induction and neural induction. These will be useful for the correct targeting of genetic manipulations of early regulatory events.