Lysosomal storage disorders are inborn diseases resulting from the lack or activity of lysosomal hydrolases, transporters, or integral membrane proteins. Although most of the genes encoding these proteins have been characterized and many gene defects identified, the molecular bases underlying the pathophysiology of these genetic diseases still remain obscure. In this mini-review, the potential role of apoptotic cell death in the development of the cellular and tissue lesions seen in lysosomal storage disorders, and particularly in neurological diseases, is discussed. A list of observations documenting either a decrease or an exacerbation in apoptosis induction are presented. The putative, yet controversial contribution of certain sphingolipids and cathepsins in the regulation of these phenomena is emphasized.