Background To enhance the sensitivity and specificity of the clinical diagnosis of progressive supranuclear palsy (PSP), neuroradiological parameters established in pathologically proven cases are needed. Methods We examined brainstem atrophy in five pathologically confirmed PSP patients (three men, mean age at death 77 years, range 64–84 years). Time interval between symptom onset and MRI ranged from 1 to 5 years, and between MRI and death from 33 to 52 months. Only one patient had clinical diagnosis of PSP at the time of MRI. Control group consisted of 19 age- and gendermatched healthy subjects. Seventeen morphometric parameters of the midbrain and pons were measured on T1-weighted midsagittal and T2-weighted axial MRI scans with Image Analyzer. Measurements of superior cerebellar peduncle (SCP) width were performed on PSP autopsy specimens. Results Mean SCP width on MRI in PSP (2.7 ± 0.8 mm, 95%CI: 2.1–3.3) was smaller than in controls (3.7 ± 0.5 mm, 95%CI: 3.5–3.9). Mean SCP width at autopsy was 8% smaller than mean SCP width on MRI. Midsagittal midbrain area in PSP (99.1 ± 6.9 mm 2 , 95%CI: 90.5–107.6) was smaller than in controls (141.0 ± 18.1 mm 2 , 95%CI: 132.2–149.7). Midbrain/pons area ratio in PSP was 1:5 and in controls was 1:4 (p < 0.01). Repeat MRI 17 months later in one PSP case revealed 30% decrease of SCP width. Conclusions MR imaging with quantitative analysis may be useful in the diagnosis of early PSP and in monitoring disease course.