Overall brain size is strikingly heritable throughout life. The influence of genes on variation in focal gray and white matter density is less pronounced and may vary with age. This paper describes the relative influences of genes and environment on variation in white matter microstructure, measured along fiber tracts with diffusion tensor imaging and magnetization transfer imaging, in a sample of 185 nine-year old children from monozygotic and dizygotic twin pairs. Fractional anisotropy, a measure of microstructural directionality, was not significantly influenced by genetic factors. In contrast, studying longitudinal and radial diffusivity separately, we found significant genetic effects for both radial and longitudinal diffusivity in the genu and splenium of the corpus callosum and the right superior longitudinal fasciculus. Moreover, genetic factors influencing the magnetization transfer ratio (MTR), putatively representing myelination, were most pronounced in the splenium of the corpus callosum and the superior longitudinal fasciculi, located posterior in the brain. The differences in the extent to which genetic and environmental factors influence the various diffusion parameters and MTR, suggest that different physiological mechanisms (either genetic or environmental) underlie these traits at nine years of age. © 2010 Elsevier Inc.