A number of devastating human disorders, for example Alzheimer's disease (AD), Hungtington's diseases, type 2 diabetes and transmissible spongiform encephalopathies (TSEs), are associated with the abnormal folding and assembly of proteins. The net result of this misfolding is the formation of large insoluble protein deposits and small toxic protein particles in a state called amyloid. What are the molecular mechanisms that govern the amyloid fibrils’ potential to seed the formation of new aggregates that propagate the amyloid state, and to damage cells in amyloid-associated diseases? We have developed approaches that are capable of resolving the fibril particle concentrations, their length distributions, as well as their toxic potential to cells. With these approaches, we have shown that the disease-associated properties of amyloid can be linked to small nano-sized amyloid particles created through the breakage of amyloid fibrils. The approaches we have developed offer new opportunities to determine, quantify, and predict the course and the consequences in amyloid assembly of cytotoxic as well as functional amyloid systems.