Indiana University-Purdue University Indianapolis (IUPUI) / Fetal alcohol spectrum disorder is a disease caused by prenatal alcohol exposure. It is characterized by craniofacial abnormalities, growth retardation, central nervous system defects, learning disabilities and a variety of other minor defects. Even though it affects 2-5% of individuals born every year, very little is known about the mechanisms that cause it. The zebrafish (Danio rerio) presents as an interesting and efficient model for studying this disease. This study provides some insight into the mechanisms underlying observed FASD phenotypes and, more specifically, the transcription factor elf3, which is downregulated in response to ethanol exposure during early embryonic development. Here we show a number of elf3 target genes that are downregulated during early development in response to ethanol exposure. We also give some insight into the expression pattern of elf3 in relation to zygotic genome activation. Translation blocking morpholino oligonucleotides were used to implicate Elf3 in epiboly movements during gastrulation and zebrafish tail development. Taken together these results help to strengthen the zebrafish as a model for FASD in addition to giving greater insight into both the expression pattern and role of Elf3 during development.