The primary root of Arabidopsis thaliana has a remarkably uniform cellular organisation. The fixed radial pattern of cell types in the mature root arises from proliferative divisions within the root meristem. The root meristem, in turn, is laid down during embryogenesis. We have analysed six mutations causing alterations in the radial organisation of the root. Embryonic phenotypes resulting from wooden leg, gallum, pinocchio, scarecrow, short root and fass mutations are described. While mutations in the fass gene affect morphogenesis of all cells, the five other mutations cause alterations in specific layers. Wooden leg and gollum mutations interfere with the proper organisation of the vascular tissue. Shortroot, scarecrow and pinocchio affect the endodermis and cortex. The layer-specific phenotypes caused by all five mutations are also apparent in the hypocotyl. All these phenotypes originate from defects in the radial organisation of the embryonic axis. Secondary roots, which are formed post-embryonically, also display layer-specific phenotypes.