<p>  Fetal Alcohol Syndrome (FAS) is the most serious form of Fetal Alcohol Spectrum Disorders (FASD) and the most prevalent neurodevelopmental disorder in North America. Patients with FAS may exhibit cognitive problems with working memory, manipulating information, and reduced executive functioning. Additionally, previous studies exhibited that stress responses are affected by prenatal alcohol consumption Gut microbiota compositions can also influence stress responses and memory, as several studies have shown strong relationships between the enteric gut system and the brain. However, few studies have examined how prenatal alcohol exposure’s effects on the gut microbiome and neuroinflammatory responses. For this study, pregnant HsdBlu:LE Long Evans rats were treated with either a dry diet, liquid diet, or liquid diet with alcohol. On day 28 and 42 after birth, three male and three female adolescent pups from each treatment group had their gut microbiome (fecal samples) analyzed through 16S rRNA amplicon sequencing. Brain histology staining of the cortex and hippocampus regions was also done to evaluate changes in the CNS through microglial counts and morphology analysis. There were no significant differences in alpha diversity of the fecal microbiome between groups of pups based on prenatal alcohol exposure (PAE), sex, age, the interaction of PAE and sex, or in the morphology of cortex microglia. However, analysis of beta diversity using Bray-Curtis dissimilarity and weighted UniFrac suggested distinct microbial communities between the treatment groups based on PAE and the interaction of PAE, sex, and the interaction between PAE and sex. Microglial count comparisons by PAE or sex were only statistically different in the cortex (p ≤ 0.005). The significance of this study suggests that there are some associations between the gut microbiome and CNS inflammation in rats with PAE. Based on these findings, 11 future studies may implement therapeutics such as antibiotics or probiotics to mitigate cognitive or neural symptoms of FASD affected individuals. </p>