Transmissible spongiform encephalopathies are a group of fatal neurodegenerative diseases with long incubation time. This group includes Creutzfeld-Jakob disease, kuru, scrapie, chronic wasting disease, and bovine spongiform encephalopathy. Sensitive and specific detection of abnormal prion protein as a source agent of the above-mentioned diseases in blood could provide a diagnostic test or a screening assay for animal and human prion protein diseases diagnostics. Therefore, diagnostic tests for prion protein diseases represent unique challenge requiring development of novel assays exploiting properties of prion protein complex. Presently, diagnostic methods such as protein misfolding cyclic amplification, conformation-dependent immunoassay, dissociation-enhanced lanthanide fluorescent immunoassay, fluorescence correlation spectroscopy, and/or flow microbead immunoassay are used for abnormal prion protein (PrPSc) detection. On the other hand, using of CE for PrPSc detection in body fluids is an attractive alternative; it has been already applied for the blood samples of infected sheep, elk, chimpanzee, as well as humans. In this review, assays for prion protein detection are summarized with special attention to capillary electromigration based techniques, such as CE, CIEF, and/or CGE. The potential of the miniaturized and integrated lab-on-chip devices is highlighted, emphasizing recent advances of this field in the proteomic analysis.