We used quantal dose-titration of a mouse-adapted human transmissible spongiform encephalopathy strain (M470) to compare different analytical methods for their ability to detect asymptomatic brain prion infection after low dose inoculation. At a time point approximately 2.5-fold beyond the mean incubation period of high dose inocula, asymptomatic brain infection was commonly observed using histologic examination, Western blot, and "blind" bioassay following intracerebral inoculation with low titer inocula. At this time point, when a clinical end-point titration would usually be determined, evidence of infection was seen in all healthy animals inoculated with up to 100-fold lower inoculation doses than the lowest causing consistent clinical disease. For the assessment of the presence of asymptomatic infection, we compared different Western immunoblot and histopathological methods in relation to "blind" bioassay using transgenic Tga/20 mice overexpressing mouse prion protein (PrP). Sodium phosphotungstic acid (NaPTA) precipitation of protease-resistant PrP isoforms (PrP(res)) prior to Western blotting was found to approach the sensitivity of the Tga/20 bioassay and was superior to conventional Western blot and histopathological methods, wherein infectivity was commonly found when both of the latter were negative. Re-scaling the original titer by incorporating "blind" transmission data from surviving asymptomatic mice revises the estimate two orders of magnitude higher than the value derived using the conventional clinical disease outcome approach. We also found that the sensitivity of the NaPTA Western blot technique, if used with a diluent such as PBS compared with 10% normal brain homogenate, is adversely affected by up to around 20-fold. We postulate that infectious titer estimates based on more sensitive detection systems such as we report provide a more accurate indication of ultimate transmission risk.