The direct effects of ethanol and caffeine on embryogenesis were investigated using the whole rat embryo culture system. Compared to control embryos, the crown-rump length, number of somites, branchial bars, and morphological score were significantly reduced in embryos exposed to ethanol, caffeine, or both substances. Development of the craniofacial region, cardiac primordium and forelimb was delayed following ethanol treatment. Compared to the controls, the anterior neuropore lagged in development following caffeine treatment; closure of the posterior neuropore was significantly delayed in each of the treatment groups. The optic and olfactory primordia were not affected. The results indicate that alcohol and caffeine independently affect the embryo, but when combined their effects were not potentiated.