Previous investigations using linear CT measures found no evidence of caudate atrophy in asymptomatic persons who have the DNA haplotype linked to the Huntington's disease (HD) gene. We measured volumes of the caudate, putamen, and globus pallidus on MRIs of 10 gene marker-positive and 18 gene marker-negative asymptomatic at-risk persons. The volumes of all basal ganglia structures were significantly reduced in the marker-positive group, even after controlling for age, total brain volume, and minor neurologic signs. Discriminant function analysis using basal ganglia volumes and age as predictor variables correctly identified genetic status in 86% of subjects. These results indicate that basal ganglia volume is reduced before individuals become symptomatic with HD.