During amphibian embryogenesis, axis definition and the specification of the mesoderm and neural plate depend on cell interactions. These interactions are mediated by peptide growth factors and other diffusible molecules including retinoic acid (RA). Several genes encoding transcription factors are known to be immediate early or delayed early responses to the action of growth factors and retinoids in the embryo. By the criterion of cycloheximide (CHX) resistance, goosecoid (gsc), Xlim-1, Xbra, Mix.1, XFKH1/pintallavis/XFD1, and Xnot are immediate early response genes in mesoderm/induction. Among these, gsc, Xnot and XFKH1 are superinduced by CHX, suggesting that their regulation depends in part on rapid turnover of the mRNA. RA is known to induce Xlim-1 in Xenopus embryos and to lead to anterior malformations. We show that 9-cis RA, the ligand of the RXR receptor class, is more effective than all-trans RA in generating these biological effects.