Iron overload results in an accumulation of electron-dense iron-containing particles (IPs) such as ferritin and hemosiderin within the lysosomes of rat liver cells. In order to evaluate the effect or iron overload on lysosomal function, efforts were made to isolate lysosomes with different iron contents by means of ultracentrifugation in Percoll and Metrizamide gradients. Lysosomes isolated on the Percoll gradient were characterized ultrastructurally by a uniform matrix consisting mainly of IPs and these lysosomes contained a high iron concentration and showed a very low proteolytic activity. They may, therefore, constitute, or be equated, with a special type of residual bodies. They were also fragile, as judged by their significant release of enzymes during incubation in vitro. Lysosomes isolated in the Metrizamide gradient contained remnants of sequestered organelles and some IPs. These organelles displayed a somewhat impeded proteolytic activity compared with control lysosomes, as well as preserved membrane stability during incubation in vitro. We suggest that these may be precursors of the heavily iron-laden lysosomes recovered in the Percoll gradient. Our findings demonstrate that different populations of lysosomes exist in iron-overloaded rat liver cells, which show specific characteristics with regard to ultrastructural appearance, iron content and proteolytic activity. Differing iron contents is the most likely reason for their diverging densities and membrane integrities, whereas the difference in proteolytic activity could be a result of varying amounts of degradable substrate.