Prions are composed of the misfolded prion protein (PrP Sc) organized in a variety of aggregates. An important question in the prion field has been to determine the identity of functional PrP Sc aggregates. In this study, we used equilibrium sedimentation in sucrose density gradients to separate PrP Sc aggregates from three hamster prion strains (Hyper, Drowsy, SSLOW) subjected to minimal manipulations. We show that PrP Sc aggregates distribute in a wide range of arrangements and the relative proportion of each species depends on the prion strain. We observed a direct correlation between the density of the predominant PrP Sc aggregates and the incubation periods for the strains studied. The relative presence of PrP Sc in fractions of different sucrose densities was indicative of the protein deposits present in the brain as analyzed by histology. Interestingly, no association was found between sensitivity to proteolytic degradation and aggregation profiles. Therefore, the organization of PrP molecules in terms of the density of aggregates generated may determine some of the particular strain properties, whereas others are independent from it. Our findings may contribute to understand the mechanisms of strain variation and the role of PrP Sc aggregates in prion-induced neurodegeneration.