Glycosphingolipid storage disorders are inborn errors of metabolism caused by the defective activity of degradative enzymes in lysosomes. In this review, we summarize studies performed over the past few years attempting to define the secondary and down-stream biochemical and cellular pathways affected in GSL storage disorders that are responsible for neuronal dysfunction, a characteristic of most of these disorders. We focus mainly on the regulation of intracellular calcium homeostasis and phospholipid biosynthesis. These studies may help unravel new roles for glycosphingolipids in the regulation of normal cell physiology, as well as suggest potential new therapeutic options in the glycosphingolipid and other lysosomal storage disorders.