Although abnormal processing of amyloid precursor protein (APP) leads to early onset of Alzheimer's disease, the normal function of this protein is poorly understood. APP is widely expressed in axons, dendrites, and synapses in both central and peripheral nervous systems. Mice homozygous for APP or its homologue APP-like protein 2 (APLP2) null mutation (KO) are viable, but double mutants for APP and APLP2 deletions (DKO) are early postnatal lethal. To investigate the role of APP in synapse development, we compared the ultrastructure of submandibular ganglion synapses between DKO and littermate APLP2 KO mice at birth. Using serial electron microscopy, we found that the size of presynaptic boutons and the number of active zones per bouton were comparable in both strains of animals. However, the synaptic vesicle density, active zone size, and docked vesicle number per active zone were significantly reduced in DKO compared to those in APLP2 KO. These results indicate that the APP family of proteins plays an important role in regulating the formation and function of inter-neuronal synapses.