Accumulating evidence suggests that the endo-lysosomal system provides a substantial store of Ca2+ that is tapped by the Ca2+-mobilizing messenger, NAADP. In this article, we review evidence that NAADP-mediated Ca2+ release from this acidic Ca2+ store proceeds through activation of the newly described two-pore channels (TPCs). We discuss recent advances in defining the sub-cellular targeting, topology and biophysics of TPCs. We also discuss physiological roles and the evolution of this ubiquitous ion channel family. © 2011 Elsevier Ltd.