Background: Despite an increasing number of studies, findings of structural brain alterations in patients with Tourette syndrome are still inconsistent. Several confounders (comorbid conditions, medication, gender, age, IQ) might explain these discrepancies. In the present study, these confounders were excluded to identify differences in basal ganglia and corpus callosum size that can be ascribed more probably to Tourette syndrome per se. Methods: High-resolution T1-weighted structural magnetic resonance images of 49 boys with Tourette syndrome were compared with those of 42 healthy boys. The groups were matched for IQ and age (9 to 15 years). Boys with comorbid conditions and previous treatment were excluded. Volumes of gray and white matter, cerebrospinal fluid as well as the size of the basal ganglia, the thalamus, the corpus callosum and its subregions were estimated. Results: The left and right putamen and subregion 3 of the corpus callosum were larger in boys with Tourette syndrome than in healthy controls. No differences were found in volumes of caudate nucleus, globus pallidus or thalamus of each hemisphere or in total callosal size and its other subregions. Conclusions: Bilateral enlargement of the putamen may reflect dopaminergic dysfunction or neuroimmunologic alterations (PANDAS) underlying Tourette syndrome. The larger callosal motor subregion 3 might be a consequence of daily tic activity. Previous divergent volumetric findings might be ascribed to confounding variables like comorbid conditions or medication, or to different imaging methods.