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Early to mid‐adolescence is an important developmental period for subcortical brain maturation, but longitudinal studies of these neurodevelopmental changes are lacking. The present study acquired repeated magnetic resonance images from 60 adolescent subjects (28 female) at ages 12.5 and 16.5 years to map changes in subcortical structure volumes. Automated segmentation techniques optimized for longitudinal measurement were used to delineate volumes of the caudate, putamen, nucleus accumbens, pallidum, hippocampus, thalamus and the whole brain. Amygdala volumes were described using manual tracing methods. The results revealed heterogeneous maturation across the regions of interest (ROIs), and change was differentially moderated by sex and hemisphere. The caudate, thalamus and putamen declined in volume, more for females relative to males, and decreases in the putamen and …