Bone morphogenetic protein 4 (BMP-4) is expressed in the ventral marginal zone of the gastrulating embryo. At late gastrula stage this gene is expressed in the ventral-most part of the slit blastopore and in tissues that derive from it. At tailbud stages BMP-4 is expressed in the spinal cord roof plate, neural crest, eye and auditory vesicle. The interactions of BMP-4 with dorsal genes such as goosecoid (gsc) and Xnot-2 were studied in vivo. In embryos ventralized by UV irradiation and suramin treatment, BMP-4 zygotic transcripts accumulate prematurely and the entire marginal zone expresses this gene. The patterning effect of BMP-4 on ventro-posterior development can be revealed by a sensitive assay involving the injection of BMP-4 mRNA in the ventral marginal zone of embryos partially dorsalized with LiCl, which leads to the complete rescue of trunk and tail structures. The experiments presented here argue that BMP-4 may act in vivo as a ventral signal for the proper patterning of the marginal zone, actively interacting with dorsal genes such as gsc and Xnot-2. A model is proposed in which the timing of expression of various marginal zone-specific genes plays a central role in patterning the mesoderm.