We describe a novel phenotype in Arabidopsis embryos homozygous for the temperature-sensitive topless-1 mutation. This mutation causes the transformation of the shoot pole into a root. Developing topless embryos fail to express markers for the shoot apical meristem (SHOOT MERISTEMLESS and UNUSUAL FLORAL ORGANS) and the hypocotyl (KNAT1). By contrast, the pattern of expression of root markers is either duplicated (LENNY, J1092) or expanded (SCARECROW). Shifts of developing topless embryos between permissive and restrictive temperatures show that apical fates (cotyledons plus shoot apical meristem) can be transformed to basal fates (root) as late as transition stage. As the apical pole of transition stage embryos shows both morphological and molecular characteristics of shoot development, this demonstrates that the topless 1 mutation is capable of causing structures specified as shoot to be respecified as root. Finally, our experiments fail to show a clear link between auxin signal transduction and topless-1 mutant activity: the development of the apical root in topless mutant individuals is not dependent on the activity of the predicted auxin response factor MONOPTEROS nor is the expression of DR5, a proposed 'auxin maximum reporter', expanded in the apical domain of topless embryos.