About 7.5million adults in Germany cannot read and write properly despite attending school for several years. They are considered to be functional illiterates. Since the ability to read and write is crucial for being employed and socially accepted, we developed a literacy training to overcome these deficits. In this study, we investigate the structural changes induced by the training. A group of 20 functional illiterates and 20 adult normal readers participated in the study. Group differences as well as intervention-related changes in gray (voxel-based morphometry, VBM) and white matter (Tract-Based Spatial Statistics, TBSS, applied to fractional anisotropy, FA, obtained with diffusion tensor imaging, DTI) were assessed in functional illiterates and normal reading controls. VBM analyses revealed decreased gray matter intensities in functional illiterates compared to normal readers before training in several reading-related brain regions such as the superior temporal gyrus, supramarginal gyrus, and angular gyrus. Using TBSS, functional illiterates showed reduced FA values in the genu of the corpus callosum. After training, both the gray matter intensities and FA values increased in functional illiterates and were no longer statistically different from controls' pre-test data. Moreover, the increase was positively correlated with reading and writing skills. The findings suggest that poor literacy skills are associated with several structural abnormalities in reading-related brain areas. In addition, we showed that while literacy skills of functional illiterates improved after training, the structural differences to controls disappeared.