Intracellular inclusions seen by the pathologist may have variable significance. Although they are excellent markers of proteolytic disorders, they can also be due to several other mechanisms. This article examines recent data on the morphology, significance and consequences of aging lipofuscins in the brain and retina, neurofibrillary tangles and Lewy bodies, and Birbeck granules associated with Langerhans histiocytosis. Some of these disorders involve increased protein production, misfolding and aggregation, and altered intracellular proteolysis, but other cell constituents may also play a role. Proteolytic mechanisms do not appear to be involved in the formation of Birbeck granules, which helped to reveal the Langerhans origin of histiocytosis X. Analyses of intracellular inclusions, together with genetic and epigenetic studies, are highly informative in various degenerative diseases.