The lysosome is an organelle primarily engaged in the hydrolysis of soluble substrates of intracellular and extracellular origin. Thus, the lysosome is the recipient of a great amount of plasma membrane that must be eliminated in order to maintain its normal size. In the eukaryotic cell, the plasma membrane is composed of large quantities of sphingolipids, and for that reason the eukaryotic lysosome contains a complete set of hydrolases and activator proteins specialized in the degradation of both glycosphingolipids and sphingomyelin. In order to protect its integrity from the indiscriminate action of these hydrolases, the lysosome acquired protective integral lysosomal membrane proteins and a system designed to extrude excess membranes destined for degradation into its luminal space. When an enzyme and/or its activator protein are mutated, the specific sphingolipid substrate accumulates in the lumen of the lysosome, leading to the development of a lysosomal storage disorder (LSD) or sphingolipidosis. In this review we describe structural and ultrastructural features of these disorders as potential diagnostic tools. We also illustrate methods that are normally utilized to study the molecular biology of lysosomes and that have potential applications in the study of LSDs