Purification of scrapie prions from hamster brains has demonstrated that the infectious particles contain one major protein, PrP 27-30. This protein, which is required for and inseparable from scrapie infectivity, polymerizes into heterogeneous rod-shaped particles measuring 10-20 nm in diameter and 100-200 nm in length. We attempted to identify the minimal infectious unit by disrupting aggregates of the rods. Prolonged sonication resulted in progressive fragmentation of the rods into spherical particles with a mean diameter of 19 nm and short rods with a mean length of 60 nm. No change in scrapie infectivity accompanied this profound alteration in rod morphology. In contrast, brief sonication disrupted the ultrastructure of the filamentous bacteriophage M13 and led to a marked loss in infectivity. No consistent correlation could be made between scrapie prion infectivity and disruption of the rods by a variety of treatments. Proteases, acid, base, chaotropic agents, detergents, and heat were examined for their ability to alter the morphology of the rods. The lack of correlation between ultrastructural morphology of the rods and titers of prions is consistent with the hypothesis that the rods are aggregates of prions and are not fundamental particles themselves.