We studied the emergence of vesicle pool organization at developing hippocampal synapses by monitoring vesicle recycling and neurotransmitter release as well as examining electron micrographs. Our analysis suggests that presynaptic boutons go through three distinct functional states to mature. At the onset the synapses lack readily releasable vesicles although they possess a pool of recycling vesicles that can release neurotransmitters under strong stimulation. In the next stage the majority of these recycling vesicles switches to a functionally docked state and forms the readily releasable pool (RRP). After assembly of the RRP, new vesicles build the reserve pool. At the mature state the size of the RRP increases linearly with increasing recycling pool size. Furthermore, this preferential filling of the RRP during early synapse maturation is reduced strikingly in synapses deficient in synapsin I and II. Taken together, these results expose a mechanism that ensures functionally effective allocation of a limited number of vesicles in a CNS synapse.