The pattern of Pax-2 expression was studied in Danforth's short tail homozygous mice using Pax-2-specific antibodies. Because these mice lack a notochord in caudal regions, the floor plate of the spinal cord is not induced and posterior mesoderm-derived structures are also affected. The expression of Pax-2 during neural differentiation in the spinal cord was normal in anterior sections, but ectopic expression in the ventral half of the basal plate was observed in regions lacking the floor plate. The data support the hypothesis that Pax-2 expression domains are influenced by signals emanating from the floor plate and that Pax-2 functions during the dorsal-ventral patterning of the spinal cord. In the developing excretory system, Pax-2 expression was normal in the anterior structures, such as the mesonephros, and in the mesonephric duct. However, Pax-2 was not expressed in the uninduced metanephric mesenchyme. Thus, activation of Pax-2 in the mesenchyme is an early response to inductive signals emanating from the ureter. The Danforth's short tail mutation is a useful model for the study of developmentally regulated genes that are under the influence of the notochord or floor plate.