Lysosomes are organelles in eukaryotic cells that contain digestive enzymes to digest macromolecules. They are built in the Golgi apparatus. At pH 4.8, the interior of the lysosomes is more acidic than the cytosol (pH 7). The lysosome single membrane stabilizes the low pH by pumping in protons (H⁺) from the cytosol, and also protects the cytosol, and therefore the rest of the cell, from the degradative enzymes within the lysosome. The digestive enzymes need the acidic environment of the lysosome to function correctly. All these enzymes are produced in the endoplasmic reticulum, and transported and processed through the Golgi apparatus. The Golgi apparatus produces lysosomes by budding.

The most important enzymes in lysosomes are:

• Lipase, which digests lipids,
• Carbohydrases , which digest carbohydrates (e.g., sugars),
• Proteases, which digest proteins,
• Nucleases, which digest nucleic acids.

The lysosomes are used for the digestion of macromolecules from phagocytosis (ingestion of cells), from the cell's own recycling process (where old components such as worn out mitochondria are continuously destroyed and replaced by new ones, and receptor proteins are recycled), and for autophagic cell death, a form of programmed self-destruction of the cell, which means that the cell is digesting itself. Other functions include digesting foreign bacteria that invade a cell and helping repair damage to the plasma membrane by serving as a membrane patch, sealing the wound.

There are a number of illnesses that are caused by the malfunction of the lysosomes or one of their digestive proteins, e.g., Tay-Sachs disease, or Pompe's disease. These are caused by a defective or missing digestive protein, which leads to the accumulation of substrates within the cell, resulting in impaired cell metabolism. Broadly, these can be classified as mucopolysaccharidoses, GM₂ gangliosidoses , lipid storage disorders , glycoproteinoses , mucolipidoses , or leukodystrophies .

The constant pH of 4.8 is maintained by hydrogen ion pumps and Cl- ion channels.