The most complex and the same time the most interesting entity in the universe, the brain, remains largely enigmatic. The building blocks of it, neurons, are highly specialized processing units that together underlie more complex processes. Neurons communicate with each other via synapses, where they exchange information. This information exchange needs to be very precise and is tightly controlled in space and time. In order to their sophisticated jobs, neurons depend on a highly specialized morphology. To send information to other neurons, evolution has engineered the axon, a long prolongation of the cell membrane that resembles a wire. The axon is efficient at propagating electric signals because they do not require the transfer of mass, however transport of proteins and organelles to support the extended axons and distant synapses is a challenge. The problem is that the exact mechanisms that orchestrate and regulate the transport of active zone precursors are far from being fully understood. In my doctoral research, I analyzed the cellular machinery and processes that organize axonal transport. Drosophila melanogaster is a highly suitable model to understand these processes. Particularly, the larval stage is highly accessible to intravital and super- resolution light microscopy techniques, while the abundance of genetic tools allows for dissection of the various elements in an unprecedented manner. By using fluorescent tags to label synaptic proteins, I was able to quantitatively characterize their transport to the synaptic terminal in the living intact animal. Moreover, the genetic tools that the Drosophila community has elaborated allowed to generate mutants of different proteins involved in the process to see how transport and synapse function are affected when they are absent or altered. In the current work, I present evidence that presynaptic biogenesis is mediated by axonal co-transport of active zone proteins and synaptic vesicle proteins in a new organelle that resembles lysosomes, we named PLV (presynaptic lysosome-related vesicle). By intravital in vivo imaging of Drosophila larvae, we have been able to see how synaptic proteins and active zone components are transported together with proteins of the lysosomal pathway. Furthermore, we show how Arl8, a kinesin adaptor for lyososomal transport, is also required for proper transport of synaptic proteins. Loss of Arl8 results in the depletion of synaptic proteins at the presynaptic sites, which in turn leads to impaired neurotransmission. In the absence of Arl8, the PLVs accumulate in neuronal cell bodies and hardly any axonal transport can be observed. The characterization of these accumulations showed that these vesicles are around 70 nm in diameter, and are positive for synaptic markers as well as active zone proteins. Conversely, up regulation of Arl8 results in an increase in axonal transport of PLVs proteins and presynaptic function is facilitated. These data was supported by experiments in mouse models with comparable results. To conclude, this work reveals an unexpected function for a lysosome-related organelle as the basic building block for presynaptic biogenesis and contributes to a better understanding of axonal transport.