Xenopus FoxD3 (XFD-6) is an intron-less gene initially expressed within the Spemann organizer and later in premigratory neural crest cells. Based upon sequence and expression pattern comparisons, it represents the Xenopus orthologue to zebrafish fkd6, chicken CWH-3 and mammalian HFH-2 (genesis). Early expression of FoxD3 is activated by the Wnt-pathway and inhibited by BMP signalling. Ectopic overexpression of FoxD3 leads to an enlargement of the neural plate concomitant with a failure in neural crest formation, loss of anterior structures, lack of closure of the neural tube and severe defects in somitogenesis. Phenotypic variation is accompanied by down-regulation of neural crest markers, including Xslug, Xtwist and Xcadherin-11. FoxD3 also inhibits its own expression, thereby acting in a negative autoregulatory loop. By injections of VP16 and engrailed fusions we can demonstrate that FoxD3 acts as a negative transcriptional regulator; this repressive function strictly requires the presence of the winged helix domain. Transplantation experiments show that FoxD3 overexpressing cells from the prospective neural crest do neither differentiate nor migrate.