Ultrastructural correlates of synaptic and dendritic spines loss have never been studied in detail in human transmissible spongiform encephalopathies (TSEs)-Creutzfeldt-Jakob disease (CJD), Gerstmann-Sträussler-Scheinker (GSS) disease and fatal familial insomnia (FFI). In this paper, we describe synaptic alterations as found in brain biopsies from Creutzfeldt-Jakob disease and fatal familial insomnia patients. Our material consisted of brain biopsies obtained by open surgery from one FFI case, one case of variant Creutzfeldt-Jakob disease (vCJD), seven cases of sporadic Creutzfeldt-Jakob disease (sCJD) and one case of iatrogenic (human growth hormone) Creutzfeldt-Jakob disease (iCJD). For electron microscopy, approximately 2mm(3) samples were immersion fixed in 2.5% glutaraldehyde for less than 24h, embedded in Epon and routinely processed. Grids were examined and photographed in a transmission electron microscope. The synaptic alterations were found constantly; in practically every brain biopsy they were frequent. The accumulation of different subcellular organelles (neuroaxonal dystrophy), dark synapses and branching cisterns were the most frequent findings while concentric arrays of membranes were only rarely found. Autophagic vacuoles are formed in many synapses in all categories of human transmissible encephalopathies. We conclude that synaptic autophagy contributes to overall synaptic loss in brains affected in prion diseases.