DNA methylation is an important epigenetic factor that participates in silencing genes. Genomic approaches to studying DNA methylation promise to be particularly fruitful, since DNA methylation is involved in global control of gene expression in many organisms. With its draft genome completed and a large quantity of available cDNA data, Ciona intestinalis is newly emerging as an invaluable model organism for investigating genome-wide gene expression and function. Here we examine the effects of 5-aza-2′-deoxycytidine (5-aza-CdR), a chemical that blocks CpG methylation, on the gene expression profile of early C. intestinalis embryos, using oligonucleotide-based microarray analysis. Embryos treated with 5-aza-CdR show delayed gastrulation and are developmentally arrested at the neurula stage. They subsequently lose cellular adhesion and finally die. Apoptosis was not detected in these embryos by TUNEL staining at 12 h, indicating that the defects observed did not result from 5-aza-CdR-induced apoptosis. Gene expression profiles of 12-h-old 5-aza-CdR-treated embryos compared to wild-type revealed 91 upregulated genes and 168 downreg-ulated genes. Although nearly half of these encoded proteins with unknown functions, several encoded cell-signaling molecules and transcription factors. In addition, genes associated with the stress response and cell defense were upregulated, whereas genes involved in cell adhesion were downregulated.