Objective Previously, the novel peptides NAPVSIPQ and SALLRSIPA were shown to prevent alcohol-induced fetal death and growth abnormalities in a mouse model of fetal alcohol syndrome. This study evaluated whether these peptides could prevent long-term alcohol-induced learning abnormalities. In addition, because specific cytokines are known to effect long-term potentiation, a model of learning at the molecular level, we studied the effect of these novel peptides on tumor necrosis factor–α, interleukin-6, and interferon-γ levels. Study design We used a well-characterized mouse model of fetal alcohol syndrome. Pregnant mice were injected on day 8 with alcohol (0.03 mL/kg) or placebo. Pretreatment with NAPVSIPQ + SALLRSIPA (20 μg) or placebo was given 30 minutes before alcohol. Embryos were removed after 6 hours, at which time cytokine, tumor necrosis factor–α, interleukin-6, and interferon-γ levels were measured with enzyme-linked immunoassays. To test spatial learning, adult offspring from litters that were treated with alcohol, control, NAPVSIPQ + SALLRSIPA then alcohol, or NAPVSIPQ + SALLRSIPA alone were evaluated for latency to find a hidden platform in the Morris water maze. Results Alcohol treatment increased tumor necrosis factor–α levels versus control levels (50.0 ± 3.5 pg/mL vs 32.7 ± 2.4 pg/mL; P < .001). NAPVSIPQ + SALLRSIPA pretreatment prevented this increase (39.9 9 ± 2.8 pg/mL; P ≤ .01), with levels similar to control ( P = .1). Similarly, alcohol increased interleukin-6 levels versus control levels (22.6 ± 1.4 pg/mL vs 17.3 ± 0.6 pg/mL; P < .001), and NAPVSIPQ + SALLRSIPA prevented this increase (19.1 ± 1.0 pg/mL; P ≤ .02), with levels similar to control levels ( P = .2). Interferon-γ levels were not different among the 3 groups (alcohol, 14.6 ± 4.9 pg/mL; control, 17.9 ± 6.6 pg/mL; alcohol + NAPVSIPQ + SALLRSIPA, 13.6 ± 4.9 pg/mL; P = .2). In the Morris water maze, alcohol-treated groups did not learn over the 7-day trial compared with the control group ( P = .001). Groups that were pretreated with NAPVSIPQ + SALLRSIPA then alcohol learned significantly, which was similar to the control group. Groups that were treated with only NAPVSIPQ + SALLRSIPA learned significantly earlier, with the shortest latency once learning commenced. Conclusion The peptides, NAPVSIPQ + SALLRSIPA, prevented the alcohol-induced spatial learning deficits and attenuated alcohol-induced proinflammatory cytokine increase in a model of fetal alcohol syndrome. This study demonstrates the peptides' significant in vivo efficacy with long-lasting effects obtained after prenatal administration.