Potentially teratogenic agents enter the environment at a rate that greatly exceeds current capabilities to effectively evaluate their reproductive toxicities. This is due, in part, to costly, labour-intensive methodologies involving mammalian embryonic screening assays that are currently in use worldwide. Therefore, we sought to develop a rapid, less expensive screening system with which to identify molecular biomarkers of teratogenicity using a non-mammalian system. Embryos of the topminnow, Fundulus heteroclitus, offer several advantages in terms of reproductive toxicity screening efficiency as compared with mammalian embryonic systems. These embryos are easily manipulated and develop normally at ambient temperature in air, water, or air-saturated mineral oils, making them readily adapted for field studies. In the present study, developing F. heteroclitus embryos were exposed to teratogenic concentrations of sodium valproate (VPA) or arsenic acid (arsenate), and the frequency and types of induced malformations were evaluated. Using in situ transcription and antisense RNA (aRNA) amplification procedures (IST/aRNA), we attempted to correlate the teratogenic outcomes to specific alterations in the expression of a panel of developmentally regulated genes. Preliminary studies identified treatment concentrations of arsenate and VPA that induced abnormal development in 95% of the surviving embryos. Among the F. heteroclitus embryos, the structural defects most commonly induced by these compounds were cardiac and neural tube malformations, The genetic expression profiles revealed a number of genes whose expression levels were significantly altered by exposure to the test compounds. Molecular analysis of F. heteroclitus embryonic development represents a novel, inexpensive approach to screen for potential teratogens, and identify genes whose expression patterns may be used as biomarkers, or indicators, of teratogenicity.