Lysosomes are intracytoplasmic organelles containing 60 different hydrolases that function in the digestion of intracellular and extracellular substrates. These organelles also have a set of integral membrane proteins, proton transporters, as well as a number of proteins from different cellular compartments such as the plasma membrane, endosome and the Golgi apparatus. A new view is emerging in which the lysosome is no longer considered as only a terminal degradation compartment. In fact lysosomes are implicated in other specialized cellular processes such as antigen presentation, bone remodeling, and functional regulation of various growth factors. This review examines the biogenesis of lysosomes, the contribution of different organelles to their formation and the exquisite mechanisms of protein sorting mediated by specific receptors. This review also discusses the implication of mutations that affect soluble hydrolases, lysosomal activator proteins, sorting receptors and proteins associated to the sorting machinery. Most of these mutations have an effect on the physical and mental development of humans as a result of storage disorders that lead to the accumulation of one or more undigested substrates in the lysosomes.