In the synthesis and trafficking of precursors of most lysosomal matrix proteins, the stages necessary for lysosomal delivery include the addition of phosphorylated mannose-rich oligosaccharides, binding of the modified proteins to receptors, their segregation from the secretory pathways and delivery to the endosomal pathway. Targeting of both internally synthesized and externally provided enzymes (as in enzyme replacement therapy) to endosomes is executed by a complex machinery of membrane and cytosolic proteins. Recently, the homotypic fusion and vacuolar protein sorting (HOPS) complex has been identified in lysosomes from human cells. This complex is likely to play an important role in the exchange of enzymes between endosomal and lysosomal compartments. The present review describes the interactions and functions of proteins that participate in delivering lysosomal proteins to different lysosomal compartments. In summary, lysosomal trafficking depends on the recognition of many structural signals. It delivers soluble and membrane proteins, and can be exploited for therapeutic substitution of missing enzymes.