Brain magnetic resonance images (MRI) of 104 healthy children and adolescents, aged 4–18, showed significant effects of age and gender on brain morphometry. Males had larger cerebral (9%) and cerebellar (8%) volumes (P < 0.0001 and P = 0.008. respectively), which remained significant even after correction for height and weight After adjusting for cerebral size, the putamen and globus pallidus remained larger in males, while relative caudate size was larger in females. Neither cerebral nor cerebellar volume changed significantly across this age range. Lateral ventricular volume increased significantly in males (trend for females), with males showing an increase in slope after age 11. In males only, caudate and putamen decreased with age (P = 0.007 and 0.05, respectively). The left lateral ventricles and putamen were significantly greater than the right P = 0.01 and 0.0001, respectively). In contrast, the cerebral hemispheres and caudate showed a highly consistent right greater-than-left asymmetry (P < 0.0001 for both). All volumes demonstrated a high degree of variability. These findings highlight gender-specific maturational changes of the developing brain and the need for large gender-matched samples in pediatric neuropsychiatric studies.