The process of moving proteins and organelles along the axon is essential for neuronal survival and function, ensuring proper communication between the cell body and distant synapses. The efficient and precise delivery of proteins via axon transport is critical for processes ranging from synaptic plasticity and neurotransmission to neuronal growth and maintenance. However, the identities of all the transported proteins have only recently begun to be investigated. Retinal ganglion cells (RGCs) provide a unique opportunity for access to central nervous system (CNS) axons as the retina is located outside the brain in the eye, with long axonal projections (~1 cm in mouse) that innervate the brain. We have developed and optimized methods for unbiased in vivo protein labeling in rodent RGC somata with intravitreal N-hydroxysuccinimido (NHS)-biotin and subsequent visualization of transported proteins along the optic nerve using confocal microscopy. Here, we describe these procedures in detail.