FoxH1 (Fast1) was first characterized as the transcriptional partner for Smad proteins. Together with Smad2/4, it forms the activin response factor(ARF) that binds to the Mix.2 promoter in Xenopus embryos. Foxh1 is expressed maternally in Xenopus . Depletion of maternal Foxh1 mRNA results in abnormalities of head and dorsal axis formation. We show that FoxH1 is required, together with XTcf3/β catenin,to activate the zygotic expression of the nodal gene, Xnr3 in a Smad2-independent manner. In contrast, maternal FoxH1 acts as an inhibitor of Xnr5 and 6 transcription, preventing their upregulation on the ventral side of the embryo, by the maternal T-box transcription factor VegT. We conclude that maternal FoxH1 has essential, context-dependent roles in regulating the pattern of zygotic gene expression in the early embryo.