Fetal alcohol spectrum disorders (FASD) encompass a broad range of effects caused by prenatal alcohol exposure. In the United States, conservative estimates place the incidence of FASD at a rate of 5 in 100 births. Children with FASD can have morphological afflictions including congenital defects of the brain, spinal cord, heart, eyes, and skeleton, as well as poor formation of facial structures such as the nose and mouth. Cognitive and behavioral abnormalities such as learning disabilities, socio-developmental delays and emotional disorders are also highly prevalent. There is no known cure for FASD and in utero detection methods are not available. In terms of urinary tract defects, kidney and renal related maladies may represent underreported aspects of FASD. To better understand the renal phenotypes associated with prenatal alcohol exposure, we employed the zebrafish, Danio rerio, a vertebrate species well suited for developmental nephrology and teratological work that has been used extensively to model FASD. We treated zebrafish embryos with ethanol then examined pattern formation and physiological activity of nephrons, which are the basic structural and functional unit of the kidney. Using whole mount in situ hybridization, we found that the formation of several cell types in the nephron blood filter and tubule, as well as renal progenitor populations, were perturbed by alcohol exposure. Interestingly, supplementation with all-trans retinoic acid, a vitamin A derivative associated with mitigating the effects of ethanol exposure in zebrafish and other animals, was sufficient to completely or partially rescue multiple ethanol induced kidney cell defects and restore nephron physiological activity. These studies have revealed several consequences of ethanol exposure that lead to the deregulation of renal ontogeny, and implicate a key role for reduced RA levels, thereby contributing useful insights relevant to the broader field of FASD research.