Magnetic resonance (MR) techniques enable in vivo measurement of the atrophy of the brainstem and cerebellum in spinocerebellar ataxia type 1 (SCA1) and 2 (SCA2) patients, which is accompanied by a decrease in the concentration of N-acetyl aspartate (NAA) or of the NAA/creatine ratio in the pons and cerebellum. Mean diffusivity (D) is emerging as an additional sensitive and quantitative MR parameter to investigate brain diseases. In order to explore differences between the MR features of SCA1 and SCA2 and correlate the MR and clinical findings in the two conditions, we examined 16 SCA1 patients, 12 SCA2 patients and 20 healthy control subjects. The MR protocol included T1-weighted 3D gradient echo sequences, single-voxel proton spectroscopy of the right cerebellar hemisphere (dentate and peridentate region) and of the pons with a PRESS sequence and an external reference quantitation method, and (in nine patients with SCA1 and nine patients with SCA2) diffusion-weighted echo-planar images with reconstruction of the D maps. The patients were evaluated with the Inherited Ataxia Clinical Rating Scale (IACRS). Compared with control subjects, the SCA1 and SCA2 patients showed a decrease (P < 0.01) in the volume of the brainstem and cerebellum and in the concentration of NAA in the pons and cerebellar hemisphere, whereas D of the brainstem and cerebellum was increased. No significant difference was observed between the SCA1 and SCA2 patient groups. No correlation between cerebellar volume and dentate and peridentate NAA concentration was found in SCA1 or SCA2 patients. The volume of the brainstem, D of the brainstem and cerebellum and the concentration of NAA in the pons were correlated (P < 0.05) with the IACRS score in SCA1 but not in SCA2. This discrepancy is in line with the clinical observation that the clinical deficit has a later onset and faster progression in SCA1 and an earlier onset and slower progression in SCA2, and suggests that neurodegeneration of the brainstem is a comparatively more rapid process in SCA1. In conclusion, our study indicates that SCA1 and SCA2 substantially exhibit the same MR features. The correlation in SCA1 between clinical severity and quantitative volumetric, diffusion MRI and proton MR spectroscopy findings in the brainstem indicates that these measurements might be employed for longitudinal studies and hopefully as surrogate markers in future pharmacological trials of this condition.