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Here we investigate the effects of prenatal exposure to methamphetamine on local brain volume using magnetic resonance imaging. Because many who use MA during pregnancy also use alcohol, a known teratogen, we examined whether local brain volumes differed among 61 children , 21 with prenatal MA exposure, 18 with concomitant prenatal alcohol exposure, 13 with heavy prenatal alcohol but not MA exposure, and 27 unexposed controls. Volume reductions were observed in both exposure groups relative to controls in striatal and thalamic regions bilaterally and in right prefrontal and left occipitoparietal cortices. Striatal volume reductions were more severe in the MAA group than in the ALC group and within the MAA group, a negative correlation between full-scale intelligence quotient scores and caudate volume was observed. Limbic structures, including the anterior and posterior cingulate, the inferior frontal gyrus, and ventral and lateral temporal lobes bilaterally, were increased in volume in both exposure groups. These findings suggest that striatal and limbic structures know to be sites of neurotoxicity in adult MA abusers may be more vulnerable to prenatal MA exposure than alcohol exposure and that more severe striatal damage is associated with more severe cognitive deficit.