During the later developmental stages of both central and peripheral nervous systems, axonal branches and synapses are massively reorganized to form mature connections. Although it is a classically-known process, the morphology at single axon level and the molecular mechanisms are not fully understood due to technical difficulties which come from the complexity of neural circuitry. Here, with a combination of sparse expression system and tissue clearing method, we revealed the morphological characteristics of axonal reorganization in developing chick ciliary ganglion (CG), a conventional model system of synaptic development. Plasmid vectors, which express tdTomato under the modulation of sparse expression promoter Thy1s (Ako et al, 2011), were introduced into the midbrain presynaptic neuron using in ovo electroporation method (Odani et al, 2008). The CG was isolated at E8-14, cleared with ScaleA2 protocol (Hama et al, 2011) and imaged as a whole under two-photon microscopy. Each intertangled axon was three-dimensionally traced and quantitatively analyzed. We found that the total length and branching number of the axons are gradually decreased with development and that many axons lose their branches before E14. Our results were complementary to the previous electromicroscopic/electrophysiological studies carried out by Landmesser and Pilar in 1970s which showed the decrease in presynaptic inputs from multiple to single during E8-14. It is suggested that the excess presynaptic branches are pruned to form one-to-one connections without any "winners" of the synaptic competition which form oligopoly connections over postsynaptic targets. With the combination of genetic manipulations, our system of developmental connectomics would facilitate further understanding of the fundamental principles and molecular mechanisms underlying developmental axonal reorganization.