Genetic factors are involved in variation in fetal alcohol spectrum disorders (FASD), which is also observed among various inbred mouse strains. The CD1 mouse strain is often used in toxicological and genetic experiments. However, there is little literature using this strain to study long-term neurologic abnormalities of FASD. In the present study, we addressed the effect of prenatal ethanol exposure on neurological alterations in adult CD1 mice. The female CD1 mice received exposure to ethanol solution (10 vol%) starting from 2 weeks before mating up to pups born (postnatal day 1). At 24 weeks after the birth, the prenatal ethanol-exposed mice and control mice showed no difference in spatial learning and memory performance in a Morris water maze. Consistently, pathological changes, such as increased neuronal apoptosis, decreased synaptic protein synaptophysin expression, synaptic loss and reactive astrogliosis, were not observed in the hippocampus of mice prenatally exposed to ethanol. These results suggest that CD1 mice are highly resistant to prenatal alcohol exposure and may serve as genetic modification models of FASD.