<p>Cryo-electron microscopy studies on amyloid fibrils formed by different proteins and isolated from the brains of persons with neurodegenerative diseases have consistently shown that their core structure is distinct from that of fibrils formed by the same proteins in cell-free systems. Attempts to replicate brain-derived amyloid fibrils in vitro have thus far fallen short of faithfully reproducing their structure, post-translational modifications and pathological properties. Whether this discrepancy is a major contributing factor to the poor clinical translation of antiamyloid therapies and diagnostics remains uncertain, partially because the structure of amyloid fibrils formed in the commonly used preclinical models remains unknown. This article presents (1) an overview of recent advances and progress toward reproducing disease-relevant pathological aggregates in vitro and in preclinical models of neurodegenerative diseases; (2) an experimental strategy to determine the structure of fibrils from these models; and (3) recommendations for optimizing their use to bridge the translational gap and support the development of more effective therapies. Establishing that the process of fibrillization and inclusion formation can be faithfully recapitulated in preclinical models is also crucial for enhancing their translational relevance and to guide the development of disease-relevant diagnostics and therapeutics. Until native fibrils can be produced at scale, the choice of which type of fibril preparation to use should be guided by the specific research question and intended application as different applications may warrant different levels of biochemical and structural similarity to disease-derived fibrils.</p>