Boutons are specialised presynaptic compartments that lie along the axons of central neurons. Release of neurotransmitter from boutons is tightly regulated by the level of intracellular calcium [Ca2+]i. A rise in Ca2+ level may be generated in several ways; entry of extracellular Ca2+ via voltage gated calcium channels (VGCCs), entry via ligand-operated channels (LOCs) or the release of Ca2+ from intracellular Ca2+ stores. The role of Ca2+ stores in boutons remains poorly understood, despite recent work indicating that the release of Ca2+ from the endoplasmic reticulum (ER) may contribute to transmitter release. In this study we assess whether the lysosome or a closely related organelle functions as a Ca2+ store in the boutons of hippocampal pyramidal neurones. Lysosomes are small acidic organelles more commonly known for their role in degrading redundant cellular constituents. Using a fluorescent lysosomal marker, we show that lysosomes are located in the axons of hippocampal CA3 neurones. Selective pharmacological lysis of the lysosomes with glycyl-phenylalanine 2-naphthylamide (GPN) generates rapid, highly focal Ca2+ transients within the axon and increases the frequency of spontaneous miniature excitatory post-synaptic currents (mEPSCs), revealing that the organelle contains Ca2+ at a concentration sufficient to evoke transmitter release. Confocal laser scanning microscopy, combined with electrophysiology is used to monitor the action potential evoked increases in [Ca2+]i in boutons. We show that disruption of lysosomes compromises action potential evoked [Ca2+]i but this effect is occluded if the ER is discharged. Conversely, disruption of the lysosome does not appear to impact on the capacity of the ER to release Ca2+. These results suggest that the lysosome may serve as a Ca2+ store within hippocampal boutons, with a Ca2+ signalling role that is unique from that of the ER.