Tourette syndrome (TS) is a neuropsychiatric disorder with the cardinal symptoms of motor and vocal tics. The onset occurs during childhood; many patients experience a subsequent reduction of tic frequency and severity suggesting that the pathways involved play a significant developmental role. Research has mainly focused on the cortico-striato-thalamo-cortical circuit, but clinical symptoms and recent neuroimaging studies suggest the involvement of limbic structures as well. We acquired diffusion-weighted data at 1.5T in fifteen adult patients fulfilling the DSM-IV-TR criteria for TS and in a healthy control group. Based on the Harvard–Oxford subcortical structural atlas we investigated the microstructure of grey matter nuclei such as the nucleus accumbens, the amygdala, the putamen, the pallidum and the thalamus. The basal ganglia and the thalamus show in the direct comparison between patients and control subjects no significant differences in the diffusion indices. However, within the Tourette group the correlation coefficients between diffusion parameters and measures of tic severity indicate that the individual microstructure of the basal ganglia has an influence on the individual clinical phenotype. The microstructure assessment of the amygdala and nucleus accumbens in TS revealed a significant difference for the left nucleus accumbens and the right amygdala. Our findings suggest two pathophysiologic patterns in TS. One pattern could indicate altered connectivity based on the correlation between the increased mean and axial diffusivity in the basal ganglia and tic severity. The other pattern is characterized by the increase in radial diffusivity in the amygdala and the correlation between radial diffusivity in the nucleus accumbens and tic measures indicating potentially altered myelination.