The pons is one of the brain areas demonstrating selective degeneration in Machado-Joseph disease (MJD), which is caused by the expansion of a polyglutamine stretch in the protein called ataxin-3. Although the resultant pontine atrophy is readily recognized by magnetic resonance imaging (MRI), the features and natural process of atrophy are not fully understood. To characterize them, we analyzed the midsagittal images of the pons obtained by MRI. We found a difference in atrophy between the pontine base and tegmentum. The reduced size of the pontine tegmentum was prominent early after the onset of clinical symptoms. No overlap was seen in the range of the area of pontine tegmentum between MJD and controls. The quotient of atrophy of the pontine tegmentum divided by age correlated well with the CAG repeat number. In contrast, the area of the pontine base correlated negatively with disease duration. Particularly, the size of the pontine base remained in the range of controls for a relatively long time after the onset of symptoms. These results suggest that the atrophic process is not uniform in the pons in MJD and that the different patterns of atrophy may be derived from the differential vulnerability in pontine structures.