Nodal signals play important roles in mesendoderm induction, establishment of left-right asymmetry and anteroposterior patterning of the neuroectoderm during vertebrate embryogenesis. It is aimed at identifying Nodal-regulated genes in zebrafish embryos, particularly those encoding transcription factors. A (Affymetrix) genechip analysis was performed using RNAs derived from embryos injected with squint mRNA, MZoep mutant embryos that are deficient in Nodal signaling, and wildtype embryos at the 30% epiboly stage. Transcripts (genes) with at least two-fold changes in expression level between wildtype and the other samples were identified. In squint mRNA-injected embryos, 265 transcripts show an increased expression level and 111 have a decreased expression level; in MZoep embryos, the expression of 1 495 transcripts increases while 550 transcripts express at a decreased level. Furthermore, overexpression of squint causes increased expression of 26 and decreased expression of 11 annotated transcription factor genes; in MZoep embryos, the number of transcription factor genes showing an increase and decrease of expression are 69 and 30, respectively. These results would provide useful information for further studying mechanisms and biological functions of Nodal signal transduction.