Mutations in presenilins (PS), transmembrane proteins encoding the catalytic subunit of γ-secretase, result in familial Alzheimer’s disease (FAD). Several studies have identified lysosomal defects in cells lacking PS or expressing FAD-associated PS mutations, which have been previously attributed to a function for PS in lysosomal acidification. Now, in this issue, Coen et al. (2012. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201201076) provide a series of results that challenge this idea and propose instead that presenilins play a role in calcium-mediated lysosomal fusion.