We investigated whether the brainstem is affected by the pathologic process of sporadic Creutzfeldt-Jakob disease (sCJD), with particular attention to brainstem atrophy, neuronal loss, pyramidal tract degeneration, and prion protein (PrP) deposition, in 33 patients with sCJD. Brainstem atrophy, particularly in the pontine base, was relatively prominent in patients with disease of unusually prolonged duration. Neuronal loss and pyramidal tract degeneration were also identified in some but not all patients with prolonged disease. Neuronal loss was relatively prominent in the pontine nucleus and less so in the substantia nigra and inferior olivary nucleus; motor nuclei of the brainstem tegmentum were well preserved. PrP deposition was present in the brainstem in all patients, and was identified predominantly in the substantia nigra, quadrigeminal body, pontine nucleus, and inferior olivary nucleus. PrP deposition was less prominent in the red nucleus and tegmentum of the pons and medulla oblongata. PrP deposition occurred least or not at all in the pyramidal tract. The density of PrP deposition in the sCJD brainstem was not associated with disease duration or neuronal degeneration until the late stage. Our results show that atrophy, neuronal loss, and pyramidal tract degeneration occur in the sCJD brainstem, particularly in patients with an unusually prolonged disease course. These findings are not associated directly with PrP deposition and may reflect end-stage sCJD. No VV1, VV2, or MV2 cases were included in our study; however, we suggest that widespread and relatively stereotypic PrP deposition is a consistent pathologic feature of sCJD, at least in MM1 sCJD patients. Although accumulation of PrP in the brainstem appears to be an early pathologic event in sCJD, and may remain into the late disease stage, the brainstem remains relatively resistant to the pathologic process of sCJD.