Subcortical band heterotopia (SBH) is a developmental disorder in which neuroblasts migrating from the periventricular zone to the cortex cannot reach their final destination. Subcortical bands might interfere with axonal development. Therefore, this study examined white matter organization in 10 healthy controls and 2 patients with drug-resistant epilepsy (referred to as patients 1 and 2), in whom diagnostic magnetic resonance imaging revealed subcortical bands of gray matter. Diffusion tensor imaging, advanced tractography methods, and functional imaging were performed in patient 2. The number of subcortical fibers decreased significantly in both patients. The heterotopias interrupted the propagation of the tracking algorithm. Only a small number of tracts were generated from inside the heterotopias. According to the literature and our findings, SBHs appear to differ in their localization, extension, and structure. Some heterotopias might allow the propagation of tractography, thereby creating the impression that tracts are passing through, whereas others interrupt the propagation, as observed in our cases. In addition, a reduction in the number of subcortical white matter fibers was observed. These findings may have consequences in pre-surgical planning. The generalization of seizures might be facilitated by a non-reduction in SCWM fibers and tracts passing through the band, and these patients might benefit more from extensive resections of the epileptogenic zone than others.