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Aim: To quantify regional subcortical brain volume anomalies in youth with fetal alcohol spectrum disorder (FASD), assess the relative sensitivity and specificity of abnormal volumes in FASD vs. a comparison group, and examine associations with cognitive function. Method: Participants: 47 children with FASD and 39 typically-developing comparison participants, ages 8–17 years, who completed physical evaluations, cognitive and behavioral testing, and an MRI brain scan. A large normative MRI dataset that controlled for sex, age, and intracranial volume was used to quantify the developmental status of 7 bilateral subcortical regional volumes. Z-scores were calculated based on volumetric differences from the normative sample. T-tests compared subcortical volumes across groups. Percentages of atypical volumes are reported as are sensitivity and specificity in discriminating groups. Lastly, Pearson correlations examined the relationships between subcortical volumes and neurocognitive performance. Results: Participants with FASD demonstrated lower mean volumes across a majority of subcortical regions relative to the comparison group with prominent group differences in the bilateral hippocampi and bilateral caudate. More individuals with FASD (89%) had one or more abnormally small volume compared to 72% of the comparison group. The bilateral hippocampi, bilateral putamen, and right pallidum were most sensitive in discriminating those with FASD from the comparison group. Exploratory analyses revealed associations between subcortical volumes and cognitive functioning that differed across groups. Conclusion: In this sample, youth with FASD had a greater number of atypically small subcortical volumes than individuals without FASD. Findings suggest MRI may have utility in identifying individuals with structural brain anomalies resulting from PAE.