Peripheral nerve injury is a major clinical and public health challenge. Although a common and increasingly prevalent wartime condition (1), injury to peripheral nerves, plexuses, and roots is present in 5% of patients seen in civilian trauma centers (2). In one study, almost half of peripheral nerve injuries at trauma centers were due to motor vehicle accidents and about half required surgery (3). Peripheral nerve injuries can substantially impact quality of life through loss of function and increased risk of secondary disabilities from falls, fractures, and other injuries (2). Neurons are connected in intricate communication networks established during development to convey sensory information from peripheral receptors of sensory neurons to the central nervous system (the brain and spinal cord), and to convey commands from the central nervous system to effector organs such as skeletal muscle innervated by motor neurons. The peripheral nerve environment is quite complex, consisting of axonal projections from neurons, supporting cells such as Schwann cells and fibroblasts, and the blood supply to the nerve. Connective tissue known as endoneurium surrounds peripheral nerve axons. Within peripheral nerves, axons are grouped into fascicles surrounded by connective tissue known as perineurium. Between and surrounding groups of fascicles is the epineurium. Microvessel plexuses course longitudinally through the epineurium and send branches through the perineurium to form a vascular network of capillaries in the endoneurium (4). The primary supporting cell for peripheral nerves is the Schwann cell. Schwann cells wrap around axons in a spiral fashion multiple times and their plasma membranes form a lipid-rich tubular cover around the axon known as the myelin sheath or the neurilemma. Schwann cells and the myelin sheath support and maintain axons and help to guide axons during axonal regeneration following nerve injury (5). It has been known for quite some time that regenerating axons exhibit a strong preference for growing along the inside portion of remaining basal lamina tubes in the distal nerve stump, the well-characterized “bands of Bungner” (6–10). Schwann cells originally associated with myelinated axons form such bands all the way from the transection site to the distal end organ target. The critical concept here is that the eventual distal destination of regenerating axons is largely determined by the Schwann cell tubes as they enter at the nerve transection site (9,11,12). Recent elegant work with transgenic mice expressing fluorescent proteins in their axons has verified that most (but not all) regenerating axons distal to either a crush or a transection injury remain within a single Schwann cell band as they grow within the distal nerve stump (13,14). Within the motor system it has even been shown that the same axon predominantly reinnervates the same neuromuscular junctions, and that Schwann cell bands act as mechanical barriers to direct axon outgrowth (13). The neuronal cell body is the site of synthesis of virtually all proteins and organelles in the cell. A complex process known as anterograde transport continuously moves materials from the neuronal cell body via the axon to its terminal synapse. These transported substances include neurotransmitters that facilitate communications between the neuron and end organ tissue across a narrow extracellular space known as the synaptic cleft (5) or, as in the case of the motor neuron innervation of muscle, the neuromuscular junction (15). Conversely, end organs such as muscle produce substances that act as nerve growth factors. These make their way across the neuromuscular junction to the innervating motor neuron axon (16). Some of these substances, or chemical messengers induced by them, are packaged and conveyed by retrograde transport from the synapse via the axon to the neuronal cell body. In this manner, the neuron and its end organ are continuously informed about the status of the connection between them. It has been suggested that information from end organs takes the form of factors that sustain existing nerve cell connections and promote the regeneration of damaged nerve cells. For instance, it has long been known that muscle exerts a strong influence on developing and regenerating motor neurons, and we have recently shown that even within an individual muscle there are factors that can influence the accuracy of reinnervation (17). Recent work has elegantly shown that if a single muscle fiber is selectively lesioned, the motor neuron axon terminal making up the proximal side of the neuromuscular junction rapidly atrophies and withdraws from the muscle postsynaptic sites within a matter of hours (18). The clinical significance, prognosis, and treatment of peripheral nerve injury depend on the site and extent of the injury. Despite regeneration, extensive peripheral nerve injuries can result in the effective paralysis of the entire limb or distal portions of the limb. Two peripheral nerve injury classification schemes, the Seddon (19) and the Sunderland (20), are in common use. These classify nerve injury according to whether the injury was confined to demyelination only or a more severe disruption of axons and supporting connective tissue. According to Seddon, the most severe injuries are classified as axonotmesis and neurotmesis. Axonotmesis is a nerve injury characterized by axon disruption rather than destruction of the connective tissue framework. The connective tissue and Schwann tubes are relatively intact. This is typical of stretch injuries common in falls and motor vehicle accidents. In contrast, neurotmesis involves the disruption of the nerve trunk and the connective tissue structure. This would occur in injuries where the nerve has been completely severed or badly crushed. Prognosis is good in peripheral nerve injuries where endoneurial Schwann cell tubes remain intact. Disruption of the Schwann cell tubes results in the loss of established pathways that regenerating axons follow. For extensive injuries, surgery is usually necessary to remove damaged nerve tissue and join viable nerve ends by direct anastomosis or by a nerve tissue graft (1). Refinement of microsurgical techniques involving the introduction of the surgical microscope and microsutures has increased the accuracy of this mechanical process, yet only 10% of adults will recover normal nerve function using state-of-the-art current techniques (21–23). The limits of microsurgical techniques have been reached; this is not surprising given that the finest suture material and needles ( and microns, respectively) are still quite a bit larger than the smallest axons that need to be repaired. The major key to recovery of function following peripheral nerve lesions is the accurate regeneration of axons to their original target end organs. A recognized leader of clinical nerve repair once stated, “The core of the problem is not promoting axon regeneration, but in getting them back to where they belong” (Sunderland, 1991) (23). At the level of a mixed peripheral nerve where motor and sensory axons are intermixed, correct discriminatory choices for appropriate terminal nerve branches at the lesion site are necessary prerequisites for the subsequent successful reinnervation of appropriate end-organ targets. Motor axons previously innervating muscle may be misdirected to sensory organs, and sensory axons typically innervating skin can be misdirected to muscle. Misdirected regeneration is a major barrier to functional recovery. In order to understand axonal regeneration and the mechanisms that axons use to navigate to target tissues, our laboratory has conducted a series of studies that are now culminating in proteomic investigations to identify specific biochemical mediators that may be the underlying mechanisms that direct accurate axon regeneration. We describe our work and that of others in the development of a model of axonal regeneration in the rodent femoral nerve and what we have learned from it. Then we will lay out our current research direction illustrating how approaches in proteomics such as two-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry can be used to identify the underlying mediators that may lead to new therapies for peripheral nerve injury.