The murine Brachyury (T) gene is required in mesoderm formation. Mutants carrying different T alleles show a graded severity of defects correlated with gene dosage along the body axis. The phenotypes range from shortening of the tail to the malformation of sacral vertebrae in heterozygotes, and to disruption of trunk development and embryonic death in homozygotes. Defects include a severe disturbance of the primitive streak, an early cessation of mesoderm formation and absence of the allantois and notochord, the latter resulting in an abnormality of the neural tube and somites. The T gene is expressed in nascent mesoderm and in the notochord of wild-type embryos. Here the expression of T in whole-mount mutant embryos homozygous for the T allele TWis is described. The TWis gene product is altered, but the TWis/TWis phenotype is very similar to that of T/T embryos which lack T. In early TWis/TWis embryos T expression is normal, but ceases prematurely during early organogenesis coincident with a cessation of mesoderm formation. The archenteron/node region is disrupted and the extension of the notochord precursor comes to a halt, followed by a decrease and finally a complete loss of T gene expression in the primitive streak and the head process/notochord precursor. It appears that the primary defect of the mutant embryo is the disruption of the notochord precursor in the node region which is required for axis elongation. Thus the T gene product is directly or indirectly involved in the organization of axial development.