Background <p>Long-term brain atrophy and cognitive function have rarely been reported in patients without pre-existing brain disorders who survived progressive multifocal leukoencephalopathy (PML).</p> Case presentation <p>Patient 1 was a 38-year-old woman with late-onset combined immunodeficiency, who presented with progressive cognitive decline and right hemiparesis. Brain MRI revealed a hyperintense lesion in the left frontal lobe. Patient 2 was a 53-year-old man in remission from follicular lymphoma, who experienced cognitive deterioration and displayed hyperintense signals in the left frontal and bilateral posterior lobes on MRI. Brain biopsy confirmed PML in both patients. After recovering from acute neurological decline, the cognitive and physical function of the patients was followed and we retrospectively analyzed sequential alterations in the MRI over eight years. Hyperintense lesion areas, cerebral hemisphere size, and intracranial volume were measured to calculate the monthly change ratios of the brain (MCRB), along with assessment of the third ventricle width. Both patients experienced no relapse. Wechsler Memory Scale-Revised scores improved in Patient 1 but slightly declined in Patient 2 despite stable Mini-Mental State Examination scores in both patients. MRI results were classified as lesion expansion, lesion reduction, and chronic atrophy. During the chronic atrophic stage, MCRB decreased by 0.06% and 0.09% in Patients 1 and 2, respectively. The third ventricle widened by 3 and 25&#xa0;μm/month in Patients 1 and 2, respectively.</p> Conclusion <p>Progressive cerebral atrophy occurs during PML’s chronic stage, even without relapse. In these two cases, the patient with extensive bilateral lesions in the acute phase showed greater third ventricle enlargement and cognitive decline.</p>