Treatment of Xenopus blastula with activin converts undifferentiated presumptive ectoderm (animal cap) into mesoderm and endoderm in a dose-dependent manner. At low concentrations, activin induces ventral mesoderm such as blood cells. Here we show that activin-treated aggregates of animal cap cells prepared from undifferentiated presumptive ectoderm and transplanted into Xenopus embryos differentiated to form red blood cells and vascular endothelial cells. We compared gene expression profiles of the activin-treated with untreated aggregates of animal cap cells using microarray analysis. This revealed 838 clones including vascular-related genes that were expressed at levels at least 2-fold greater in the activin-treated aggregates than in the untreated controls. Of these, 356 were known Xenopus genes, 296 had homologues, and 186 were unknown genes. These findings identified novel vascular-related genes and provided insights into how the blood vessel system establishes in normal development.