Lysosomes are essentially a membrane-bound sac of hydrolytic enzymes, but they have various vital functions. Lysosomal enzymes are used to digest macromolecules, hydrolyzing proteins, polysaccharides, fats, and nucleic acids. Since the enzymes are most effective in an acidic environment, lysosomes keep their pH at approximately 5 by pumping hydrogen ions in from the cytosol. The leaking or bursting of a single lysosome will have little effect in the vast and neutral cytosol, but if several lysosomes open, the cell can be destroyed through autodigestion.

The membrane of the lysosome and the enzymes it contains are made in the rough ER and transferred by the Golgi to be tweaked. Some lysosomes are simply budded straight out from the trans face of the Golgi. The proteins of the inner membrane surface are spared from being digested by have three dimensional conformations which protect their bonds from enzymes.

One function of a lysosome is phagocytosis (from the Greek "phagein", "to eat", and "kytos", "vessel"), the process of engulfing smaller organisms or food particles. In human, macrophages (cells that move through tissue fibers) defend the body by "eating" bacteria and other invaders.

Lysosomes also engulf the cell's own material in autophagy. Cellular material is recycled when an older organelle or portion of cytosol needs to be dismantled. The organic monomers that remain are returned to the cytosol to bee reuse. The lysosome allows the cell to constant renew itself. A good example of this is the human liver cell which recycles half its macromolecules a week.

Lysosomes can even be programmed to destroy their entire cell. When cells are no longer necessary, such as the cells that make up a tadpole's tail or the webbing between a human fetus's fingers, their lysosomes dismantle them

There are many lysosomal storage diseases that can be inherited. Someone with a storage disease would lack one of the active hydrolytic enzymes normally present in a lysosome, leaving the organelle to become overfilled with indigestible substrates and unable to perform other necessary functions. In Pompe's Disease, the liver is damaged when glycogen accumulates because it cannot be broken down. In Tay-Sachs Disease, it is a lipid-digesting enzyme that is missing or inactive, allowing lipids to accumulate and impair the brain. Fortunately, storage diseases are rare.