Children with fetal alcohol syndrome (FAS) display altered performance in tasks of learning and memory, behaviours thought to be associated with the hippocampus. Altered hippocampal structure has been reported in some FAS children; therefore, a rat model system was used to determine whether the size and numbers of pyramidal cells in regions CA1 and CA3 of the hippocampal formation and granule cells in the dentate gyrus were altered by alcohol exposure during different periods of development. Rat pups were exposed to alcohol in utero during the second trimester-equivalent (E10-20), the first two trimesters-equivalent (E1-20), during the time of hippocampal pyramidal cell neurogenesis (E16-20), part of the third trimester-equivalent (P4-9), and all three trimesters-equivalent (E1-20+P4-9). Control animals (nutritional and untreated) were reared for all treatment conditions. All pups were perfused on P10. CA1 volume, pyramidal cell density, and number were reduced in pups treated with alcohol during the third trimester-equivalent, whether unique or as exposure during all three trimesters-equivalent. CA3 volume was reduced in alcohol-treated animals across all gestational ages; however, pyramidal cell density and number in this region were only reduced in animals treated with alcohol during the third trimester-equivalent. Volume of the dentate gyrus did not appear to be affected by alcohol treatment. Granule cell density and number in this region were reduced in animals treated with alcohol during the third trimester-equivalent. The third trimester-equivalent in the rat appears to be a developmental period during which the hippocampus is particularly susceptible to the effects of alcohol consumption. The resulting damage to the hippocampus may contribute to the behavioural deficits related to learning and memory noted in children with FAS.