The aim of this study was to use diffusion tensor imaging (DTI) to identify differences in the maturation of deep gray matter (GM) and white matter (WM) between patients with spina bifida cystica (SBC) (n=29) with normal-appearing brains on conventional MRI, and age-matched and sex-matched healthy control participants (n=33). Changes in DTI metrics were calculated using a log-linear regression model. We observed increasing fractional anisotropy (FA) with age in the occipital, fornix, cingulum and middle cerebellar peduncles and decreasing FA with age in the genu and splenium of the corpus callosum (CC) and caudate nuclei in patients compared to controls. Increasing FA values in some of the WM structures probably represent faulty WM maturation, whereas decreasing FA values in the CC represents changes secondary to the affected WM fibers contributing to the CC. DTI changes in deep GM and WM in the absence of any abnormality on conventional MRI might provide the basis for cognitive decline in these patients.