ABSTRACT The amyloid aggregation pathway is a multistep process, and many in vitro studies have highlighted the role of particular intermediates in the cellular toxicity of various amyloid diseases. In a previous study, we generated a yeast toxic mutant (M8) of the harmless model amyloid protein Het‐s 218‐289 . In this study, we compared the aggregation characteristics of the wild‐type (WT) and the toxic mutant at the molecular level. Both proteins formed fibrillar amyloid aggregates but with different dye‐binding properties and X‐ray diffraction patterns. The toxic amyloid formed very unusual short (80 nm) unbranched fibers visible on transmission electron microscopy. Fourier transform infrared spectroscopy demonstrated that M8 β‐sheets were essentially organized into a mixed parallel and antiparallel structure, whereas the WT protein displayed a predominantly parallel organization. Cellular toxicity may therefore be related to assembly of the toxic amyloid in a new aggregation pathway.—Berthelot, K.,Immel, F., Gean, J., Lecomte, S., Oda, R., Kauffmann, B., Cullin, C. Driving amyloid toxicity in a yeast model by structural changes: a molecular approach. FASEB J. 23, 2254–2263 (2009)