The embryonic origin of the Arabidopsis root and hypocotyl region has been investigated using histological techniques and clonal analysis. Our data reveal the pattern of cell division in the embryo giving rise to the various initials within the root promeristem. A small region of the root at its connection with the hypocotyl appears not to be derived from the promeristem initials. This region contains two cortical cell layer and [3H]thymidine incorporation data suggest that it lacks postembryonic cell divisions. Sectors marked by transposon excision from the β-glucuronidase marker gene are used to investigate cell lineages giving rise to root and hypocotyl. The position of end points from sectors with embryonic origin show little variation and hence reveal preferred positions in the seedling for cells derived from different regions of the embryo. The radial extent of complete root sectors is consistent with the radial arrangement of root meristem initials at the heart stage of embryogenesis inferred from histological analysis. Using the clonal data, a fate map is constructed depicting the destiny of heart stage embryonic cell tiers, in the seedling root and hypocotyl. The variability in the sector end points indicates that distinct cell lineages are not restricted for root or hypocotyl fate. In contrast, derivatives of the hypophyseal cell do appear to be restricted to the columella and central cell region of the root.