The Xenopus nodal related-1 (Xnr1) gene has a complex expression pattern in embryos, with two temporal phases. In the first phase, transcripts are first detected in perinuclear sites in the vegetal region of the blastula. During gastrulation, this expression disappears and transcripts become localised to the dorsal marginal zone. Expression stops and then restarts in a second phase at neurula and tailbud stages, firstly in two symmetric patches near the posterior end of the notochord, and then asymmetrically in a large domain in the left lateral plate mesoderm. In this study, we have investigated the regulation of the early phase of expression of Xnr1. We show that the T-box transcription factor VegT can induce Xnr1. It had previously been shown that Xnr1 can induce VegT in ectoderm cells and we show that the early expression of Xnr1 is regulated by an autoregulatory loop. By inspection of the Xnr1 promoter sequence, we have identified two non-palindromic T-box-binding sites, which are 10 bp apart. Using mutational analysis, we have shown that these elements are required for the VegT induction of Xnr1. The Xnr1 promoter shows striking homologies with the Xnr3 promoter. In particular, two elements that are required for Wnt signaling are conserved between these two promoters, but the two T-box sites are not conserved, and Xnr3 is not induced by VegT. A region of the promoter containing the T-box sites and the Wnt sites is sufficient to drive expression of a reporter gene in a dorsal domain in transgenic Xenopus at the gastrula stage. We show that this pattern of expression of the transgene in gastrulae is not dependent on the T-box sites.