Lysosomes originate by budding off from the membrane of the trans-Golgi network, a region of the Golgi complex responsible for sorting newly synthesized proteins, which may be designated for use in lysosomes, endosomes, or the plasma membrane. The lysosomes then fuse with membrane vesicles that derive from one of three pathways: endocytosis, autophagocytosis, and phagocytosis. In endocytosis, extracellular macromolecules are taken up into the cell to form membrane-bound vesicles called endosomes that fuse with lysosomes. Autophagocytosis is the process by which old organelles are removed from a cell; they are enveloped by internal membranes that then fuse with lysosomes. phagocytosis is carried out by specialized cells (e.g., macrophages) that engulf large extracellular particles such as dead cells or foreign invaders (e.g., bacteria) and target them for lysosomal degradation. Many of the products of lysosomal digestion, such as amino acids and nucleotides, are recycled back to the cell for use in the synthesis of new cellular components.

Lysosomal storage diseases are genetic disorders in which a genetic mutation affects the activity of one or more of the acid hydrolases. In such diseases, the normal metabolism of specific macromolecules is blocked and the macromolecules accumulate inside the lysosomes, causing severe physiological damage or deformity. Hurler's syndrome, which involves a defect in the metabolism of mucopolysaccharides, is a lysosomal storage disease.