There has been a recent explosion in research on Niemann-Pick type C disease. Much of the work has used mouse models or cells in culture to elucidate the pathophysiological mechanisms resulting in the phenotype of the disease. This work has generated several contrasting views on the mechanism, which are labeled 'controversies' here. In this review, two of these controversies are explored. The first concerns which stored materials are causative in the disease: cholesterol, gangliosides and sphingolipids, or something else? The second concerns which cells in the body require Npc1 in order to function properly: somatic cells, neurons only, or neurons and glia? For the first controversy, a clear answer has emerged. More research will be needed in order to definitively solve the second controversy.