The dominant mutation T, (Brachyury), of the T/t-complex in the mouse causes severe disorganization in neural tube, notochord, and somites in homozygotes. The use of scanning electron microscopy to investigate the relationships of cells to one another and to the extracellular matrix in the three axial organs and in the head mesenchyme reveals that cells in all areas examined are abnormal in size, shape, and arrangement in T/T embryos. Cells of T/T head mesenchyme and somites are arrayed in flat sheets of broadened cells with fewer cytoplasmic processes than those of normal littermates. The notochord is discontinuous and its surface is exposed rather than covered by a dense matrix as in the normal. Likewise the sheath of the T/T neural tube is less dense than normal. Cell size and shape are very irregular whereas normal neural tube cells are all about the same size. Extracellular matrix in T/T embryos is greatly decreased in all areas.