The organizer is a central feature of vertebrate embryogenesis and is functionally subdivided into the head organizer that gives rise primarily to the prechordal plate and induces forebrain structures, and the trunk/tail organizer that gives rise primarily to the notochord and induces more posterior structures. Goosecoid(gsc) encodes a homeodomain-containing transcription factor that is expressed in the vertebrate head organizer and prechordal plate, and can induce a secondary axis when expressed ectopically. To investigate the evolution of the vertebrate head organizer and prechordal plate, we have cloned and characterized a gsc homolog from the cephalochordate amphioxus. Amphioxus, it is important to note, lacks a prechordal plate in that the notochord extends to the extreme anterior end of the animal, and lacks elaborate differentiation of its forebrain. Gsc expression in amphioxus is initially localized during gastrulation to the mesendodermal layer of the dorsal lip of the blastopore. However, gsc expression in amphioxus is not maintained in anterior axial mesoderm, as is the case with the vertebrate prechordal plate. Rather, gsc is expressed in the dorsal axial mesoderm of the blastopore lip throughout gastrulation, appearing transiently in the presumptive notochord that underlies all regions of the amphioxus brain. The similarities in gsc expression in amphioxus and vertebrates suggest that a primitive version of the head organizer evolved prior to the origin of the vertebrates. The differences in gsc expression can be interpreted either as the loss of the prechordal plate domain in the cephalochordate lineage, or the gain of a distinct gsc-expressing prechordal plate that plays a role in forebrain induction in the vertebrate lineage.