Niemann-Pick type C disease (NPCD) is a neurodegenerative disease associated with increases in cellular cholesterol and glycolipids and most commonly caused by defective NPC1, a late endosomal protein. Using ratiometric probes we find that NPCD cells show increased endolysosomal pH. In addition U18666A, an inhibitor of NPC1, was found to increase endolysosomal pH, and the number, size and heterogeneity of endolysosomal vesicles. NPCD fibroblasts and cells treated with U18666A also show disrupted targeting of fluorescent lipid BODIPY-LacCer to high pH vesicles. Inhibiting non-lysosomal glucocerebrosidase (GBA2) reversed increases in endolysosomal pH and restored disrupted BODIPY-LacCer trafficking in NPCD fibroblasts. GBA2 KO cells also show decreased endolysosomal pH. NPCD fibroblasts also show increased expression of a key subunit of the lysosomal proton pump vATPase on GBA2 inhibition. The results are consistent with a model where both endolysosomal pH and Golgi targeting of BODIPY-LacCer are dependent on adequate levels of cytosolic-facing GlcCer, which are reduced in NPC disease. Niemann-Pick type C disease (NPCD) is a devastating neurodegenerative condition most commonly due to mutations in NPC1 [1,2] a protein of late endosomes and lysosomes [3]. (Due to difficulties in precisely distinguishing these two sets of organelles the term endolysosome will be used here to include both.) Mutations in NPC1 are associated with impaired endocytic transport via decreased endolysosomal calcium release [4,5]. In turn, endocytosis and luminal calcium are dependent on correct endolysosomal acidification [4] and have been found to be controlled by glycolipids in neurons [6], melanocytes [7], plant vacuoles [8] and C. elegans [9]. It is increasingly apparent that aberrant lysosomal GlcCer in Gaucher disease is associated with elevated endolysosomal pH [10-13]. Glycolipids, vital for mammals [14], are also implicated in membrane trafficking [10,15]. Similarly in yeast the NPC1 homologue ncr1 regulates both vacuolar pH [16] and glycolipid transport [17]. An overview of sphingolipid metabolism highlighting the connection with endocytosis is offered in Fig. S1. Does NPC1 affect endolysosomal pH? Conflicting evidence has been found both in disease fibroblasts [5,16,18-20] and in cells treated with U18666A, a putative inhibitor of NPC1 [5,21-23]. If endocytic traffic is delayed then probes which permeate all acidic organelles will show increased pH values even though fully mature lysosomes still acidify correctly. We used such a general probe to