Lysosomal storage diseases represent a group of about 50 genetic disorders caused by deficiencies of lysosomal and non-lysosomal proteins. Patients accumulate compounds which are normally degraded in the lysosome. In many diseases this accumulation affects various organs leading to severe symptoms and premature death. The revelation of the mechanism by which stored compounds affect cellular function is the basis for understanding pathophysiology underlying lysosomal storage diseases. In the past years it has become clear that storage compounds interfere with various processes on the cellular level. The spectrum covers e.g. receptor activation by non-physiologic ligands, modulation of receptor response and intracellular effectors of signal transduction cascades, impairment of autophagy, and others. Importantly, many of these processes are associated with accumulation of storage material in non-lysosomal compartments. Here we summarize current knowledge on the effects that storage material can elicit on the cellular level.