Despite different pathomechanisms, a progressive reduction of beta-cell mass underlies both type 1 and type 2 diabetes mellitus and is mainly due to increased apoptosis. Deranged ion homeostasis, cell shrinkage and intracellular acidification are early events in apoptosis, followed by executive steps including DNA degradation and loss of cell membrane integrity. We provide unprecedented evidence for the inducible, regulated and functional expression of the non-gastric H+/K+ ATPase Atp12a, an isoform of the gastric H+/K+ ATPase, in pancreatic beta-cells. This pump is expressed in a variety of cells and tissues, but its functional role is largely unknown. Among the known functions is its involvement in pH and K+ homeostasis in the distal nephron and colon. We found the expression of Atp12a in INS-1E rat insulinoma cells on the mRNA and protein level by real-time PCR and immunoblotting. Incubation of the cells in presence of SCH-28080, an inhibitor of the gastric- as well as non-gastric H+/K+ ATPase isoforms, for 24 hours led to a significant increase of annexin-V positive cells, caspase activation and induction of apoptotic cell shrinkage (apoptotic volume decrease, AVD) in absence of other apoptotic stimuli. Further we found that inhibition of the pump acts additively on the pro-apoptotic action of the short-chain fatty acid butyrate and exposure of INS-1E cells to high medium glucose (25 mM) caused a significant up-regulation of Atp12a mRNA expression. Our data indicate that the non-gastric H+/K+ ATPase has an anti-apoptotic function in beta-cells, which might be particularly relevant in a situation of nutrient excess as found in the scenario of glucolipotoxicity in the early stages of diabetes type-2 pathogenesis.