A method of detecting amyloid fibrils in biological samples utilizing flow cytometry is described. It has been found that the measurement of fluorescence from amyloidophilic dyes, such as thioflavin T and Congo red, as well as side scatter and forward scatter measurements are particularly useful in detecting the presence of amyloid fibrils. Flow cytometric detection of amyloid fibrils in subjects such as humans and livestock can be employed for diagnosis, assessment of therapeutic efficacy, research, and monitoring of livestock for the presence of infectious amyloidosis.