The polymerization of the microtubule-associated protein tau into paired helical filaments (PHFs) is one of the hallmarks of Alzheimer's disease. Insights into the prerequisites and kinetics of the polymerization was obtained by the in vitro analysis of this process. In the past, fluorescent dyes were used to stain amyloidogenic material in histology and later on similar dyes were used in in vitro studies as well. To circumvent the flaws of extragenous dyes, namely the alteration of the polymerization kinetic or incompatibility with other chemical compounds needed for stability analysis, we applied tryptophan fluorescence to the in vitro analysis of PHF formation. Single tryptophans were introduced into the hexapeptide PHF6 within the third repeat, which was shown to be involved in ß sheet formation and scattered around the whole microtubule binding domain. Tryptophan fluorescence was then used to scan the microtubule binding domain for accessibility to quenching reagent in the soluble and the aggregated state and the fluorescence resonance energy transfer (FRET) between tryptophan and tyrosine 310. Furthis approach enables the analysis of stability of PHFs in the presence of Guanidinium hydrochloride. The examples given here could be applied in modified ways to other amyloidogenic proteins.