Among the genes thought to be involved in patterning the nervous system are a family of developmentally regulated paired box-containing (Pax) genes. Mutations in some of these Pax genes lead to severe developmental abnormalities. Zebrafish pax[b](pax[zf-b]) is a member of the Pax gene family that is expressed in the presumptive posterior midbrain from the end of gastrulation and, at later stages, in other localized regions of the developing embryo. Here we show that injection of antibodies raised against the pax[b] protein causes a localized malformation at the midbrain-hindbrain boundary. In situ hybridizations demonstrate that antibody injection causes downregulation of pax[b] transcripts in the posterior midbrain and alteration of wnt-1 and eng-2 expression in this area. The data demonstrate an involvement of pax[b] in the formation of the midbrain-hindbrain junction.